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author | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2021-12-13 16:29:21 -0500 |
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committer | Maxim Cournoyer <maxim.cournoyer@gmail.com> | 2021-12-13 16:29:21 -0500 |
commit | 6dffced09ecda024e0884e352778c221ad066fd6 (patch) | |
tree | 1707e8d8df4d9c47317a39ab6abbfc2ca66a6c29 /gnu/packages/bioconductor.scm | |
parent | b603554ed044638dd40b6863d5dada59eefe03b8 (diff) | |
parent | e3196755e60ba7f1ed9d432e73f26a85e0c8893c (diff) | |
download | guix-patches-6dffced09ecda024e0884e352778c221ad066fd6.tar guix-patches-6dffced09ecda024e0884e352778c221ad066fd6.tar.gz |
Merge branch 'core-updates-frozen' into 'master'.
At last!
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r-- | gnu/packages/bioconductor.scm | 7630 |
1 files changed, 3647 insertions, 3983 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6c5b633c36..ab34958cf7 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -73,7 +73,7 @@ `((upstream-name . "org.EcK12.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.EcK12.eg.db") (synopsis "Genome wide annotation for E coli strain K12") (description @@ -103,7 +103,7 @@ analysis.") (properties `((upstream-name . "org.Bt.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/org.Bt.eg.db") (synopsis "Genome wide annotation for Bovine") (description @@ -125,7 +125,7 @@ based on mapping using Entrez Gene identifiers.") (properties `((upstream-name . "reactome.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/reactome.db/") (synopsis "Annotation maps for reactome") (description @@ -148,7 +148,7 @@ database, assembled using data from REACTOME.") `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/") (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)") @@ -171,7 +171,7 @@ taurus (UCSC version bosTau8).") `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") (synopsis "Full genome sequences for Worm") @@ -196,7 +196,7 @@ objects.") `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") (synopsis "Full genome sequences for Worm") @@ -221,7 +221,7 @@ objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") (synopsis "Full genome sequences for Fly") @@ -246,7 +246,7 @@ objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") (synopsis "Full genome sequences for Fly") @@ -271,9 +271,7 @@ Biostrings objects.") `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-dmelanogaster-ucsc-dm3" - ,r-bsgenome-dmelanogaster-ucsc-dm3))) + (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3)) (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") (synopsis "Full masked genome sequences for Fly") (description @@ -301,7 +299,7 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11") (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)") (description @@ -324,7 +322,7 @@ as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") (synopsis "Full genome sequences for Homo sapiens") @@ -347,7 +345,7 @@ as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) (build-system r-build-system) - (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) + (propagated-inputs (list r-bsgenome)) (home-page "https://bioconductor.org/packages/release/data/annotation/html/\ BSgenome.Hsapiens.NCBI.GRCh38.html") @@ -372,9 +370,7 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" - ,r-bsgenome-hsapiens-ucsc-hg19))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19)) (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") (synopsis "Full masked genome sequences for Homo sapiens") (description @@ -403,7 +399,7 @@ default.") `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") (synopsis "Full genome sequences for Mouse") @@ -427,9 +423,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-mmusculus-ucsc-mm9" - ,r-bsgenome-mmusculus-ucsc-mm9))) + (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9)) (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") (synopsis "Full masked genome sequences for Mouse") (description @@ -458,7 +452,7 @@ default." ) `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") (synopsis "Full genome sequences for Mouse") @@ -501,7 +495,7 @@ ID and species. It is used by functions in the GenomeInfoDb package.") `((upstream-name . "GO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/GO.db") (synopsis "Annotation maps describing the entire Gene Ontology") (description @@ -523,12 +517,12 @@ information about the latest version of the Gene Ontologies.") `((upstream-name . "Homo.sapiens"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene) - ("r-organismdbi" ,r-organismdbi) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures + r-go-db + r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene + r-organismdbi + r-annotationdbi)) (home-page "https://bioconductor.org/packages/Homo.sapiens/") (synopsis "Annotation package for the Homo.sapiens object") (description @@ -550,13 +544,12 @@ several related annotation packages.") (properties `((upstream-name . "Mus.musculus"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-go-db" ,r-go-db) - ("r-org-mm-eg-db" ,r-org-mm-eg-db) - ("r-organismdbi" ,r-organismdbi) - ("r-txdb-mmusculus-ucsc-mm10-knowngene" - ,r-txdb-mmusculus-ucsc-mm10-knowngene))) + (list r-annotationdbi + r-genomicfeatures + r-go-db + r-org-mm-eg-db + r-organismdbi + r-txdb-mmusculus-ucsc-mm10-knowngene)) (home-page "https://bioconductor.org/packages/Mus.musculus") (synopsis "Annotation package for the Mus.musculus object") (description @@ -578,7 +571,7 @@ from several related annotation packages.") `((upstream-name . "org.Ce.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") (synopsis "Genome wide annotation for Worm") (description @@ -600,7 +593,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.") `((upstream-name . "org.Dm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") (synopsis "Genome wide annotation for Fly") (description @@ -622,7 +615,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.") `((upstream-name . "org.Dr.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") (synopsis "Annotation for Zebrafish") (description @@ -644,7 +637,7 @@ based on mapping using Entrez Gene identifiers.") `((upstream-name . "org.Hs.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") (synopsis "Genome wide annotation for Human") (description @@ -666,7 +659,7 @@ on mapping using Entrez Gene identifiers.") `((upstream-name . "org.Mm.eg.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") (synopsis "Genome wide annotation for Mouse") (description @@ -689,7 +682,7 @@ annotations for the genome of the model mouse Mus musculus.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") (synopsis "Full genome sequences for Homo sapiens") @@ -713,7 +706,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.") `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) + (list r-bsgenome)) (home-page "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") (synopsis "Full genome sequences for Homo sapiens") @@ -737,7 +730,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") `((upstream-name . "EnsDb.Hsapiens.v75"))) (build-system r-build-system) (propagated-inputs - `(("r-ensembldb" ,r-ensembldb))) + (list r-ensembldb)) (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") (synopsis "Ensembl based annotation package") (description @@ -760,8 +753,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene") (synopsis "Annotation package for TxDb object(s)") @@ -785,7 +777,7 @@ exposing these as TxDb objects.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -810,7 +802,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) + (list r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") (synopsis "Annotation package for human genome in TxDb format") @@ -835,8 +827,7 @@ track. The database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") (synopsis "Annotation package for mouse genome in TxDb format") @@ -861,9 +852,7 @@ database is exposed as a @code{TxDb} object.") `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) + (list r-bsgenome r-genomicfeatures r-annotationdbi)) (home-page "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") @@ -890,8 +879,7 @@ based on the knownGene track.") `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-annotationdbi r-genomicfeatures)) (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") (synopsis "Annotation package for C elegans TxDb objects") (description @@ -914,11 +902,8 @@ by exposing these as TxDb objects.") `((upstream-name . "FDb.InfiniumMethylation.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") (description @@ -942,7 +927,7 @@ annotations.") `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) (build-system r-build-system) (propagated-inputs - `(("r-minfi" ,r-minfi))) + (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") (synopsis "Manifest for Illumina's EPIC methylation arrays") (description @@ -963,7 +948,7 @@ annotations.") `((upstream-name . "DO.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/DO.db/") (synopsis "Annotation maps describing the entire Disease Ontology") (description @@ -985,7 +970,7 @@ Disease Ontology.") (properties `((upstream-name . "PFAM.db"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://bioconductor.org/packages/PFAM.db") (synopsis "Set of protein ID mappings for PFAM") (description @@ -1009,12 +994,12 @@ using data from public repositories.") `((upstream-name . "phastCons100way.UCSC.hg19"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-iranges + r-s4vectors)) (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") (synopsis "UCSC phastCons conservation scores for hg19") (description @@ -1040,7 +1025,7 @@ species.") `((upstream-name . "ABAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) + (list r-annotationdbi)) (home-page "https://www.bioconductor.org/packages/ABAData/") (synopsis "Gene expression in human brain regions from Allen Brain Atlas") (description @@ -1087,29 +1072,29 @@ All datasets are restricted to protein coding genes.") "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-aneufinderdata" ,r-aneufinderdata) - ("r-ecp" ,r-ecp) - ("r-foreach" ,r-foreach) - ("r-doparallel" ,r-doparallel) - ("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-bamsignals" ,r-bamsignals) - ("r-dnacopy" ,r-dnacopy) - ("r-biostrings" ,r-biostrings) - ("r-genomicalignments" ,r-genomicalignments) - ("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2) - ("r-ggdendro" ,r-ggdendro) - ("r-ggrepel" ,r-ggrepel) - ("r-reordercluster" ,r-reordercluster) - ("r-mclust" ,r-mclust) - ("r-cowplot" ,r-cowplot))) + (list r-knitr)) + (propagated-inputs + (list r-genomicranges + r-aneufinderdata + r-ecp + r-foreach + r-doparallel + r-biocgenerics + r-s4vectors + r-genomeinfodb + r-iranges + r-rsamtools + r-bamsignals + r-dnacopy + r-biostrings + r-genomicalignments + r-ggplot2 + r-reshape2 + r-ggdendro + r-ggrepel + r-reordercluster + r-mclust + r-cowplot)) (home-page "https://bioconductor.org/packages/AneuFinder/") (synopsis "Copy number variation analysis in single-cell-sequencing data") (description "This package implements functions for copy number variant @@ -1152,10 +1137,8 @@ from Illumina 450k methylation arrays.") `((upstream-name . "biscuiteerData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-curl" ,r-curl) - ("r-experimenthub" ,r-experimenthub))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationhub r-curl r-experimenthub)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biscuiteerData") (synopsis "Data package for Biscuiteer") (description @@ -1250,8 +1233,7 @@ GenomicRanges Bioconductor package.") `((upstream-name . "geneLenDataBase"))) (build-system r-build-system) (propagated-inputs - `(("r-rtracklayer" ,r-rtracklayer) - ("r-genomicfeatures" ,r-genomicfeatures))) + (list r-rtracklayer r-genomicfeatures)) (home-page "https://bioconductor.org/packages/geneLenDataBase/") (synopsis "Lengths of mRNA transcripts for a number of genomes") (description @@ -1276,7 +1258,7 @@ genomes and gene ID formats, largely based on the UCSC table browser.") ;; make sense to build substitutes. (arguments `(#:substitutable? #f)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Experimental data for use with the genomation package") (description @@ -1299,10 +1281,7 @@ downloaded from Encode.") "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-dexseq" ,r-dexseq) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown))) + (list r-biocstyle r-dexseq r-knitr r-rmarkdown)) (home-page "https://www.bioconductor.org/packages/pasilla/") (synopsis "Data package with per-exon and per-gene read counts") (description "This package provides per-exon and per-gene read counts @@ -1353,7 +1332,7 @@ resulting in a complete gene expression profile for each cell.") (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase))) + (list r-biobase)) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description @@ -1378,7 +1357,7 @@ the form of an @code{exprSet} object.") (properties `((upstream-name . "affydata"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy))) + (list r-affy)) (home-page "https://bioconductor.org/packages/affydata/") (synopsis "Affymetrix data for demonstration purposes") (description @@ -1428,12 +1407,12 @@ yeast are also included.") `((upstream-name . "curatedTCGAData"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-experimenthub" ,r-experimenthub) - ("r-hdf5array" ,r-hdf5array) - ("r-multiassayexperiment" ,r-multiassayexperiment) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-annotationhub + r-experimenthub + r-hdf5array + r-multiassayexperiment + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/curatedTCGAData/") (synopsis "Curated data from The Cancer Genome Atlas") (description @@ -1501,12 +1480,12 @@ packages.") "0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rsamtools" ,r-rsamtools))) + (list r-s4vectors + r-iranges + r-genomicranges + r-genomicalignments + r-rtracklayer + r-rsamtools)) (home-page "https://bioconductor.org/packages/CoverageView/") (synopsis "Coverage visualization package for R") (description "This package provides a framework for the visualization of @@ -1528,16 +1507,16 @@ how the coverage distributed across the genome.") "0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fastcluster" ,r-fastcluster) - ("r-ggplot2" ,r-ggplot2) - ("r-gviz" ,r-gviz) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-fastcluster + r-ggplot2 + r-gviz + r-plyr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/cummeRbund/") (synopsis "Analyze Cufflinks high-throughput sequencing data") (description "This package allows for persistent storage, access, @@ -1559,14 +1538,14 @@ used visualizations.") "07vr27rv3z86ajd62c0ilvfgz9z35qsiwwi5pv4sygbhnnjwh3rc")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-kernsmooth" ,r-kernsmooth) - ("r-matrixstats" ,r-matrixstats) - ("r-patchwork" ,r-patchwork) - ("r-pbapply" ,r-pbapply) - ("r-statmod" ,r-statmod) - ("r-survey" ,r-survey) - ("r-viridislite" ,r-kernsmooth))) + (list r-ggplot2 + r-kernsmooth + r-matrixstats + r-patchwork + r-pbapply + r-statmod + r-survey + r-kernsmooth)) (home-page "https://github.com/borishejblum/dearseq") (synopsis "DEA for RNA-seq data through a robust variance component test") (description @@ -1588,12 +1567,12 @@ set analyses, and can deal with repeated or longitudinal data.") "0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-dbi + r-iranges + r-rsqlite + r-s4vectors + r-xvector)) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing @@ -1613,15 +1592,15 @@ biological sequences.") (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-vgam" ,r-vgam))) + (list r-biostrings + r-genomicranges + r-iranges + r-rhtslib + r-summarizedexperiment + r-variantannotation + r-vgam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/gerstung-lab/deepSNV/") (synopsis "Detection of subclonal SNVs in deep sequencing data") (description @@ -1650,13 +1629,10 @@ bases such as COSMIC.") `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) + (list r-biocgenerics r-s4vectors r-iranges r-matrix + r-matrixgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DelayedArray") (synopsis "Delayed operations on array-like objects") (description @@ -1682,11 +1658,9 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs - `(("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-iranges r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/leekgroup/derfinderHelper") (synopsis "Helper for derfinder") (description @@ -1709,17 +1683,17 @@ calculation in parallel.") (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-edger + r-genomicranges + r-ggplot2 + r-iranges + r-limma + r-mass + r-reshape2 + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DRIMSeq") (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") (description @@ -1744,15 +1718,15 @@ results.") (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs - `(("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-cluster" ,r-cluster) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocneighbors + r-biocparallel + r-cluster + r-igraph + r-matrix + r-rcpp + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily @@ -1773,12 +1747,12 @@ and evaluate clustering results.") "0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-genomeinfodb" ,r-genomeinfodb))) + (list r-biobase + r-iranges + r-genomicranges + r-rcolorbrewer + r-rtracklayer + r-genomeinfodb)) (home-page "https://bioconductor.org/packages/IdeoViz/") (synopsis "Plots data along a chromosomal ideogram") (description "This package provides functions to plot data associated with @@ -1799,8 +1773,7 @@ arbitrary genomic intervals along chromosomal ideogram.") `((upstream-name . "IRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (home-page "https://bioconductor.org/packages/IRanges") (synopsis "Infrastructure for manipulating intervals on sequences") (description @@ -1827,37 +1800,37 @@ possible.") (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-dexseq" ,r-dexseq) - ("r-dplyr" ,r-dplyr) - ("r-drimseq" ,r-drimseq) - ("r-edger" ,r-edger) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcurl" ,r-rcurl) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tximeta" ,r-tximeta) - ("r-tximport" ,r-tximport) - ("r-venndiagram" ,r-venndiagram) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-dexseq + r-dplyr + r-drimseq + r-edger + r-futile-logger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-iranges + r-limma + r-magrittr + r-plyr + r-rcolorbrewer + r-rcurl + r-readr + r-reshape2 + r-rtracklayer + r-stringr + r-tibble + r-tximeta + r-tximport + r-venndiagram + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/") (synopsis "Analyze alternative splicing in RNA-seq data") (description @@ -1881,11 +1854,7 @@ Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq" ,r-deseq) - ("r-limma" ,r-limma) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description @@ -1909,10 +1878,9 @@ absolute GSEA.") (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limsolve" ,r-limsolve))) + (list r-biobase r-limsolve)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type @@ -1939,10 +1907,8 @@ relative abundances across samples.") `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-reshape2" ,r-reshape2))) + (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb + r-reshape2)) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the @@ -1966,25 +1932,25 @@ closely reconstructs the mutational profile.") (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-bigmemory" ,r-bigmemory) ; suggested - ("r-synchronicity" ,r-synchronicity) ; suggested - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-pkgmaker" ,r-pkgmaker) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-registry" ,r-registry) - ("r-reshape2" ,r-reshape2) - ("r-rngtools" ,r-rngtools) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-cluster + r-biobase + r-biocmanager + r-bigmemory ; suggested + r-synchronicity ; suggested + r-colorspace + r-digest + r-doparallel + r-foreach + r-ggplot2 + r-gridbase + r-pkgmaker + r-rcolorbrewer + r-registry + r-reshape2 + r-rngtools + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "http://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description @@ -2009,14 +1975,14 @@ performing parallel computations on multicore machines.") "0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a")))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-preprocesscore" ,r-preprocesscore) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-preprocesscore + r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description @@ -2037,7 +2003,7 @@ analysis.") "0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/affycomp/") (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") (description @@ -2060,9 +2026,7 @@ measures for Affymetrix Oligonucleotide Arrays.") `((upstream-name . "AffyCompatible"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml))) + (list r-biostrings r-rcurl r-xml)) (home-page "https://bioconductor.org/packages/AffyCompatible/") (synopsis "Work with Affymetrix GeneChip files") (description @@ -2087,9 +2051,7 @@ Command Console} (AGCC)-compatible sample annotation files.") (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affydata" ,r-affydata) - ("r-biobase" ,r-biobase))) + (list r-affy r-affydata r-biobase)) (home-page "https://bioconductor.org/packages/affyContam/") (synopsis "Structured corruption of Affymetrix CEL file data") (description @@ -2112,27 +2074,27 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-edger" ,r-edger) - ("r-gcrma" ,r-gcrma) - ("r-glimma" ,r-glimma) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gplots" ,r-gplots) - ("r-hwriter" ,r-hwriter) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-oligoclasses" ,r-oligoclasses) - ("r-reportingtools" ,r-reportingtools) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xtable" ,r-xtable))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-edger + r-gcrma + r-glimma + r-ggplot2 + r-gostats + r-gplots + r-hwriter + r-lattice + r-limma + r-oligoclasses + r-reportingtools + r-rsqlite + r-s4vectors + r-xtable)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/affycoretools/") (synopsis "Functions for analyses with Affymetrix GeneChips") (description @@ -2153,9 +2115,9 @@ to streamline the more common analyses that a Biostatistician might see.") "02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm")))) (build-system r-build-system) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + (list r-zlibbioc)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (home-page "https://github.com/bmbolstad/affyio") (synopsis "Tools for parsing Affymetrix data files") (description @@ -2205,13 +2167,13 @@ structure.") "0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-httr" ,r-httr) - ("r-xml" ,r-xml) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-httr + r-xml + r-xtable)) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") @@ -2233,15 +2195,15 @@ microarrays.") `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-keggrest" ,r-keggrest) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-dbi + r-keggrest + r-iranges + r-rsqlite + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description @@ -2263,10 +2225,9 @@ annotation data packages using SQLite data storage.") `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-lazyeval" ,r-lazyeval))) + (list r-genomicranges r-lazyeval)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Bioconductor/AnnotationFilter") (synopsis "Facilities for filtering Bioconductor annotation resources") (description @@ -2290,16 +2251,16 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") `((upstream-name . "AnnotationForge"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-dbi + r-rcurl + r-rsqlite + r-s4vectors + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description @@ -2321,21 +2282,21 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biocversion" ,r-biocversion) - ("r-curl" ,r-curl) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-interactivedisplaybase" ,r-interactivedisplaybase) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biocversion + r-curl + r-dplyr + r-httr + r-interactivedisplaybase + r-rappdirs + r-rsqlite + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/AnnotationHub") (synopsis "Client to access AnnotationHub resources") (description @@ -2362,10 +2323,7 @@ by the user, helping with quick and reproducible access.") (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats) - ("r-r-methodss3" ,r-r-methodss3) - ("r-r-oo" ,r-r-oo) - ("r-r-utils" ,r-r-utils))) + (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils)) (home-page "https://github.com/HenrikBengtsson/aroma.light") (synopsis "Methods for normalization and visualization of microarray data") (description @@ -2388,14 +2346,14 @@ classes.") "03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-rcpp + r-rhtslib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bamsignals") (synopsis "Extract read count signals from bam files") (description @@ -2419,7 +2377,7 @@ paired-end data.") `((upstream-name . "Biobase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/Biobase") (synopsis "Base functions for Bioconductor") (description @@ -2441,17 +2399,17 @@ on Bioconductor or which replace R functions.") `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-digest" ,r-digest) - ("r-httr" ,r-httr) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) + (list r-annotationdbi + r-biocfilecache + r-digest + r-httr + r-progress + r-rappdirs + r-stringr + r-xml + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biomaRt") (synopsis "Interface to BioMart databases") (description @@ -2507,11 +2465,9 @@ powerful online queries from gene annotation to database mining.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) + (list r-futile-logger r-snow r-bh)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") (synopsis "Bioconductor facilities for parallel evaluation") (description @@ -2534,12 +2490,12 @@ objects.") `((upstream-name . "Biostrings"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-crayon + r-genomeinfodb + r-iranges + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description @@ -2562,25 +2518,25 @@ biological sequences or sets of sequences.") (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dichromat" ,r-dichromat) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-annotationdbi + r-annotationfilter + r-biocgenerics + r-biostrings + r-dichromat + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-hmisc + r-iranges + r-rcolorbrewer + r-rlang + r-rsamtools + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/biovizBase") (synopsis "Basic graphic utilities for visualization of genomic data") (description @@ -2604,16 +2560,16 @@ effort and encourages consistency.") `((upstream-name . "BSgenome"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrixstats + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/BSgenome") (synopsis "Infrastructure for Biostrings-based genome data packages") (description @@ -2635,16 +2591,16 @@ genome data packages and support for efficient SNP representation.") (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-graph" ,r-graph) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix) - ("r-rbgl" ,r-rbgl) - ("r-dbi" ,r-dbi))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-genefilter + r-graph + r-gseabase + r-matrix + r-rbgl + r-dbi)) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description @@ -2664,28 +2620,27 @@ analysis.") "1nr5p1h9131rvbpnh2kizzx9q6f4ycq6rzxy1yqg2pczqcg7hy4x")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-boot" ,r-boot) - ("r-enrichplot" ,r-enrichplot) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-dplyr" ,r-dplyr) - ("r-plotrix" ,r-plotrix) - ("r-dplyr" ,r-dplyr) - ("r-magrittr" ,r-magrittr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-txdb-hsapiens-ucsc-hg19-knowngene" - ,r-txdb-hsapiens-ucsc-hg19-knowngene))) + (list r-knitr)) + (propagated-inputs + (list r-annotationdbi + r-biocgenerics + r-boot + r-enrichplot + r-iranges + r-genomeinfodb + r-genomicranges + r-genomicfeatures + r-ggplot2 + r-gplots + r-gtools + r-dplyr + r-plotrix + r-dplyr + r-magrittr + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-txdb-hsapiens-ucsc-hg19-knowngene)) (home-page "https://www.bioconductor.org/packages/ChIPseeker/") (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization") (description "This package implements functions to retrieve the nearest @@ -2712,12 +2667,12 @@ annotation, distance to TSS, and overlap of peaks or genes.") "1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) + (list r-biocgenerics + r-genomicranges + r-iranges + r-lattice + r-s4vectors + r-shortread)) (home-page "https://bioconductor.org/packages/chipseq") (synopsis "Package for analyzing ChIPseq data") (description @@ -2740,20 +2695,20 @@ experiments.") `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-colorspace" ,r-colorspace) - ("r-digest" ,r-digest) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-getoptlong" ,r-getoptlong) - ("r-globaloptions" ,r-globaloptions) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-clue + r-colorspace + r-digest + r-doparallel + r-foreach + r-getoptlong + r-globaloptions + r-iranges + r-matrixstats + r-png + r-rcolorbrewer)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jokergoo/ComplexHeatmap") (synopsis "Making Complex Heatmaps") @@ -2778,20 +2733,20 @@ self-defined annotation graphics.") (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-chipseq" ,r-chipseq) - ("r-copyhelper" ,r-copyhelper) - ("r-data-table" ,r-data-table) - ("r-dnacopy" ,r-dnacopy) - ("r-futile-logger" ,r-futile-logger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel + r-chipseq + r-copyhelper + r-data-table + r-dnacopy + r-futile-logger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-gtools + r-iranges + r-matrixstats + r-rsamtools + r-s4vectors)) (home-page "https://github.com/PeeperLab/CopywriteR") (synopsis "Copy number information from targeted sequencing") (description @@ -2818,14 +2773,14 @@ number detection tools.") (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-lattice" ,r-lattice) - ("r-locfit" ,r-locfit) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-biocgenerics + r-genefilter + r-geneplotter + r-lattice + r-locfit + r-mass + r-rcolorbrewer)) (home-page "https://www-huber.embl.de/users/anders/DESeq/") (synopsis "Differential gene expression analysis") (description @@ -2849,21 +2804,21 @@ distribution.") (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-genefilter + r-geneplotter + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-rcpp + r-rcpparmadillo + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -2887,25 +2842,25 @@ distribution.") (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biomart + r-deseq2 + r-genefilter + r-geneplotter + r-genomicranges + r-hwriter + r-iranges + r-rcolorbrewer + r-rsamtools + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DEXSeq") (synopsis "Inference of differential exon usage in RNA-Seq") (description @@ -2933,11 +2888,9 @@ exploration of the results.") `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) + (list gsl)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/DirichletMultinomial") (synopsis "Dirichlet-Multinomial mixture models for microbiome data") (description @@ -2961,20 +2914,20 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-aroma-light" ,r-aroma-light) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-aroma-light + r-biobase + r-biocgenerics + r-biocmanager + r-biomart + r-biostrings + r-genomicfeatures + r-genomicranges + r-iranges + r-rsamtools + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/drisso/EDASeq") (synopsis "Exploratory data analysis and normalization for RNA-Seq") (description @@ -3000,10 +2953,7 @@ global-scaling and full-quantile normalization.") (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp + (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp (home-page "http://bioinf.wehi.edu.au/edgeR") (synopsis "EdgeR does empirical analysis of digital gene expression data") (description "This package can do differential expression analysis of @@ -3028,24 +2978,24 @@ CAGE.") "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-protgenerics" ,r-protgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-curl + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-protgenerics + r-rsamtools + r-rsqlite + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jotsetung/ensembldb") (synopsis "Utilities to create and use Ensembl-based annotation databases") (description @@ -3073,11 +3023,8 @@ chromosome region or transcript models of lincRNA genes.") "1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase r-biocgenerics r-genomicranges r-iranges + r-s4vectors)) (home-page "https://www.bioinf.jku.at/software/fastseg/index.html") (synopsis "Fast segmentation algorithm for genetic sequencing data") (description @@ -3103,10 +3050,7 @@ microarrays or GRanges for sequencing data.") "1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-keggrest" ,r-keggrest))) + (list r-annotationdbi r-go-db r-graph r-keggrest)) (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/" "articles/10.1186/1471-2105-10-161")) (synopsis "Generally applicable gene-set enrichment for pathway analysis") @@ -3134,14 +3078,10 @@ analysis using other methods.") "05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2")))) (build-system r-build-system) (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) + (list gfortran r-knitr)) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-survival" ,r-survival))) + (list r-annotate r-annotationdbi r-biobase r-biocgenerics + r-survival)) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description @@ -3161,8 +3101,7 @@ high-throughput sequencing experiments.") "18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm")))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-gplots" ,r-gplots))) + (list r-rcolorbrewer r-gplots)) (home-page "https://www.bioconductor.org/packages/GeneOverlap/") (synopsis "Test and visualize gene overlaps") (description "This package can be used to test two sets of gene lists @@ -3181,28 +3120,28 @@ and visualize the results.") "0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j")))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridbase" ,r-gridbase) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqpattern" ,r-seqpattern))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gridbase + r-impute + r-iranges + r-matrixstats + r-plotrix + r-plyr + r-rcpp + r-readr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqpattern)) + (native-inputs + (list r-knitr)) (home-page "https://bioinformatics.mdc-berlin.de/genomation/") (synopsis "Summary, annotation and visualization of genomic data") (description @@ -3230,13 +3169,10 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodbdata" ,r-genomeinfodbdata) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomeInfoDb") (synopsis "Utilities for manipulating chromosome identifiers") (description @@ -3260,15 +3196,15 @@ names in their natural, rather than lexicographic, order.") `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GenomicAlignments") (synopsis "Representation and manipulation of short genomic alignments") (description @@ -3293,23 +3229,23 @@ alignments.") `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocio + r-biomart + r-biostrings + r-dbi + r-genomeinfodb + r-genomicranges + r-iranges + r-rcurl + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicFeatures") (synopsis "Tools for working with transcript centric annotations") (description @@ -3337,18 +3273,18 @@ extracting the desired features in a convenient format.") (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-matrixgenerics + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) (home-page "https://bioconductor.org/packages/GenomicFiles") (synopsis "Distributed computing by file or by range") (description @@ -3371,13 +3307,9 @@ provide added flexibility for data combination and manipulation.") `((upstream-name . "GenomicRanges"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicRanges") (synopsis "Representation and manipulation of genomic intervals") (description @@ -3402,15 +3334,15 @@ manipulating genomic intervals and variables defined along a genome.") (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-annotationforge" ,r-annotationforge) - ("r-biobase" ,r-biobase) - ("r-category" ,r-category) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rbgl" ,r-rbgl))) + (list r-annotate + r-annotationdbi + r-annotationforge + r-biobase + r-category + r-go-db + r-graph + r-rgraphviz + r-rbgl)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") (description @@ -3433,14 +3365,14 @@ testing and other simple calculations.") (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-graph + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GSEABase") (synopsis "Gene set enrichment data structures and methods") (description @@ -3461,7 +3393,7 @@ Enrichment Analysis} (GSEA).") "1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from @@ -3485,12 +3417,10 @@ the Human Protein Atlas project.") ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("curl" ,curl) - ("zlib" ,zlib) ; packages using rhtslib need to link with zlib - ("r-zlibbioc" ,r-zlibbioc))) + (list curl zlib ; packages using rhtslib need to link with zlib + r-zlibbioc)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -3510,7 +3440,7 @@ of other R packages who wish to make use of HTSlib.") (base32 "0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5")))) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/impute") (synopsis "Imputation for microarray data") @@ -3534,11 +3464,9 @@ microarray data, using nearest neighbor averaging.") `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-dt" ,r-dt) - ("r-shiny" ,r-shiny))) + (list r-biocgenerics r-dt r-shiny)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/interactiveDisplayBase") (synopsis "Base package for web displays of Bioconductor objects") (description @@ -3560,11 +3488,9 @@ Shiny-based display methods for Bioconductor objects.") (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-httr" ,r-httr) - ("r-png" ,r-png))) + (list r-biostrings r-httr r-png)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/KEGGREST") (synopsis "Client-side REST access to KEGG") (description @@ -3604,27 +3530,27 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-emdbook" ,r-emdbook) - ("r-fastseg" ,r-fastseg) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-mclust" ,r-mclust) - ("r-mgcv" ,r-mgcv) - ("r-qvalue" ,r-qvalue) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-data-table + r-emdbook + r-fastseg + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-kernsmooth + r-limma + r-mclust + r-mgcv + r-qvalue + r-r-utils + r-rcpp + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-zlibbioc)) + (native-inputs + (list r-knitr)) ; for vignettes (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") @@ -3652,12 +3578,12 @@ TAB-Seq.") (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo) - ("r-xvector" ,r-xvector))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-iranges + r-seqlogo + r-xvector)) (home-page "https://bioconductor.org/packages/motifRG") (synopsis "Discover motifs in high throughput sequencing data") (description @@ -3678,32 +3604,32 @@ throughput genetic sequencing data sets using regression methods.") "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ;; These two packages are suggested packages - ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggalluvial" ,r-ggalluvial) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf) - ("r-pracma" ,r-pracma) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-variantannotation" ,r-variantannotation))) + (list r-knitr)) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-bsgenome + ;; These two packages are suggested packages + r-bsgenome-hsapiens-1000genomes-hs37d5 + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggalluvial + r-ggdendro + r-ggplot2 + r-iranges + r-magrittr + r-nmf + r-pracma + r-purrr + r-rcolorbrewer + r-s4vectors + r-stringr + r-tibble + r-tidyr + r-variantannotation)) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") (description "This package provides an extensive toolset for the @@ -3725,30 +3651,30 @@ in SNV base substitution data.") (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-digest" ,r-digest) - ("r-ggplot2" ,r-ggplot2) - ("r-impute" ,r-impute) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-maldiquant" ,r-maldiquant) - ("r-mass" ,r-mass) - ("r-mscoreutils" ,r-mscoreutils) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-pcamethods" ,r-pcamethods) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-vsn" ,r-vsn) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-affy + r-biobase + r-biocgenerics + r-biocparallel + r-digest + r-ggplot2 + r-impute + r-iranges + r-lattice + r-maldiquant + r-mass + r-mscoreutils + r-mzid + r-mzr + r-pcamethods + r-plyr + r-protgenerics + r-rcpp + r-s4vectors + r-scales + r-vsn + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description @@ -3775,32 +3701,32 @@ of mass spectrometry based proteomics data.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-msnbase" ,r-msnbase) - ("r-msmstests" ,r-msmstests) - ("r-mzid" ,r-mzid) - ("r-mzr" ,r-mzr) - ("r-protgenerics" ,r-protgenerics) - ("r-purrr" ,r-purrr) - ("r-r-cache" ,r-r-cache) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-runit" ,r-runit) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-xtable" ,r-xtable))) + (list r-annotationdbi + r-annotationhub + r-biobase + r-biocgenerics + r-biocstyle + r-biostrings + r-data-table + r-doparallel + r-dplyr + r-foreach + r-ggplot2 + r-iterators + r-msnbase + r-msmstests + r-mzid + r-mzr + r-protgenerics + r-purrr + r-r-cache + r-rcpp + r-reshape2 + r-rlang + r-runit + r-stringr + r-tibble + r-xtable)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description @@ -3827,14 +3753,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-iterators" ,r-iterators) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-xml" ,r-xml))) + (list r-doparallel + r-foreach + r-iterators + r-plyr + r-protgenerics + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description @@ -3876,20 +3802,20 @@ specific parser.") -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs - `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.28.0. - ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources - ("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ncdf4" ,r-ncdf4) - ("r-protgenerics" ,r-protgenerics) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list ;; Our default boost package won't work here, unfortunately, even with + ;; mzR version 2.28.0. + boost-for-mysql ; use this instead of the bundled boost sources + zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-ncdf4 + r-protgenerics + r-rcpp + r-rhdf5lib + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description @@ -3915,17 +3841,17 @@ previously been used in XCMS.") (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-graph" ,r-graph) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocmanager + r-dbi + r-genomicfeatures + r-genomicranges + r-graph + r-iranges + r-rbgl + r-s4vectors)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several @@ -3947,10 +3873,7 @@ the fact that each of these packages implements a select methods.") (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-biocgenerics r-mass r-rcpp)) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") (description @@ -3997,8 +3920,7 @@ proteomics packages.") (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-graph" ,r-graph))) + (list r-bh r-graph)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description @@ -4019,35 +3941,35 @@ the graph algorithms contained in the Boost library.") (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggseqlogo" ,r-ggseqlogo) - ("r-gprofiler2" ,r-gprofiler2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-pbapply" ,r-pbapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-plotrix" ,r-plotrix) - ("r-proxy" ,r-proxy) - ("r-ranger" ,r-ranger) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-s4vectors" ,r-s4vectors) - ("pandoc" ,pandoc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-cowplot + r-data-table + r-dt + r-genomation + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggseqlogo + r-gprofiler2 + r-iranges + r-knitr + r-pbapply + r-pheatmap + r-plotly + r-plotrix + r-proxy + r-ranger + r-rsqlite + r-rtracklayer + r-rmarkdown + r-s4vectors + pandoc)) + (native-inputs + (list r-knitr)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides @@ -4070,16 +3992,16 @@ library implementing most of the pipeline's features.") (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-memoise + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on @@ -4102,27 +4024,27 @@ region sets and other genomic features.") `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-category" ,r-category) - ("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gostats" ,r-gostats) - ("r-gseabase" ,r-gseabase) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-pfam-db" ,r-pfam-db) - ("r-r-utils" ,r-r-utils) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-category + r-deseq2 + r-edger + r-ggbio + r-ggplot2 + r-gostats + r-gseabase + r-hwriter + r-iranges + r-knitr + r-lattice + r-limma + r-pfam-db + r-r-utils + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -4149,10 +4071,9 @@ browser.") "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5filters r-rhdf5lib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -4179,11 +4100,11 @@ the available RAM.") (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs - `(("r-rhdf5lib" ,r-rhdf5lib))) + (list r-rhdf5lib)) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/grimbough/rhdf5filters") (synopsis "HDF5 compression filters") (description @@ -4214,16 +4135,16 @@ HDF5 datasets.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bitops + r-genomeinfodb + r-genomicranges + r-iranges + r-rhtslib + r-s4vectors + r-xvector)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") (description @@ -4249,11 +4170,7 @@ tab-delimited (tabix) files.") (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs - `(("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) + (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description @@ -4281,24 +4198,24 @@ tab-delimited (tabix) files.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocio" ,r-biocio) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-restfulr" ,r-restfulr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-biocio + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rcurl + r-restfulr + r-rsamtools + r-s4vectors + r-xml + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description @@ -4324,13 +4241,13 @@ as well as query and modify the browser state, such as the current viewport.") (properties `((upstream-name . "samr"))) (build-system r-build-system) (propagated-inputs - `(("r-gsa" ,r-gsa) - ("r-impute" ,r-impute) - ("r-matrixstats" ,r-matrixstats) - ("r-openxlsx" ,r-openxlsx) - ("r-shiny" ,r-shiny) - ("r-shinyfiles" ,r-shinyfiles))) - (native-inputs `(("gfortran" ,gfortran))) + (list r-gsa + r-impute + r-matrixstats + r-openxlsx + r-shiny + r-shinyfiles)) + (native-inputs (list gfortran)) (home-page "https://statweb.stanford.edu/~tibs/SAM/") (synopsis "Significance analysis of Microarrays") (description @@ -4352,23 +4269,23 @@ differential expression analysis, RNAseq data and related problems.") (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-xgboost" ,r-xgboost))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-igraph + r-mass + r-matrix + r-s4vectors + r-scater + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) (home-page "https://github.com/plger/scDblFinder") (synopsis "Detect multiplets in single-cell RNA sequencing data") (description @@ -4393,7 +4310,7 @@ comprehensive scDblFinder method.") (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description @@ -4416,11 +4333,7 @@ Stephens (1990).") `((upstream-name . "seqPattern"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plotrix" ,r-plotrix))) + (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix)) (home-page "https://bioconductor.org/packages/seqPattern") (synopsis "Visualising oligonucleotide patterns and motif occurrences") (description @@ -4443,24 +4356,24 @@ reference point and sorted by a user defined feature.") (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list zlib)) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-rhtslib + r-hwriter + r-iranges + r-lattice + r-latticeextra + r-rsamtools + r-s4vectors + r-xvector + r-zlibbioc)) (home-page "https://bioconductor.org/packages/ShortRead") (synopsis "FASTQ input and manipulation tools") (description @@ -4487,22 +4400,22 @@ ungapped alignment formats.") `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-circlize" ,r-circlize) - ("r-clue" ,r-clue) - ("r-cluster" ,r-cluster) - ("r-complexheatmap" ,r-complexheatmap) - ("r-digest" ,r-digest) - ("r-getoptlong" ,r-getoptlong) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-matrix" ,r-matrix) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-proxyc" ,r-proxyc) - ("r-slam" ,r-slam) - ("r-tm" ,r-tm))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-circlize + r-clue + r-cluster + r-complexheatmap + r-digest + r-getoptlong + r-go-db + r-gosemsim + r-matrix + r-org-hs-eg-db + r-proxyc + r-slam + r-tm)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/simplifyEnrichment") (synopsis "Simplify functional enrichment results") (description "This package provides a new clustering algorithm, binary @@ -4526,12 +4439,9 @@ and comparing the clusterings.") `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-igraph r-matrix r-s4vectors r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/TrajectoryUtils") (synopsis "Single-cell trajectory analysis utilities") (description @@ -4553,15 +4463,15 @@ structures to hold pseudotime inference results.") "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrixstats" ,r-matrixstats) - ("r-princurve" ,r-princurve) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-trajectoryutils" ,r-trajectoryutils))) + (list r-igraph + r-matrixstats + r-princurve + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-trajectoryutils)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/slingshot") (synopsis "Tools for ordering single-cell sequencing") (description "This package provides functions for inferring continuous, @@ -4586,15 +4496,15 @@ graph construction.") (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-hash" ,r-hash) - ("r-igraph" ,r-igraph) - ("r-plotrix" ,r-plotrix) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcurl" ,r-rcurl) - ("r-sqldf" ,r-sqldf))) + (list r-gplots + r-hash + r-igraph + r-plotrix + r-plyr + r-png + r-rcolorbrewer + r-rcurl + r-sqldf)) (home-page "https://git.bioconductor.org/packages/STRINGdb") (synopsis "Search tool for the retrieval of interacting proteins database") (description @@ -4618,22 +4528,22 @@ that integrates the various evidences.") (base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biostrings + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/") (synopsis "R package designed to simplify structural variant analysis") (description @@ -4657,17 +4567,17 @@ involving two separate genomic loci encoded as GRanges objects.") `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biobase + r-biocgenerics + r-delayedarray + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-matrixgenerics + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") (description @@ -4690,12 +4600,12 @@ samples.") "0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj")))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv) - ("r-biocparallel" ,r-biocparallel) - ("r-matrixstats" ,r-matrixstats) - ("r-limma" ,r-limma))) + (list r-edger + r-genefilter + r-mgcv + r-biocparallel + r-matrixstats + r-limma)) (home-page "https://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -4722,21 +4632,21 @@ unmodeled, or latent sources of noise.") (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-crayon" ,r-crayon) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-magrittr" ,r-magrittr) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-crayon + r-genomicranges + r-ggplot2 + r-htmlwidgets + r-magrittr + r-rsamtools + r-s4vectors + r-shortread + r-stringr + r-summarizedexperiment + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/tgirke/systemPipeR") (synopsis "Next generation sequencing workflow and reporting environment") (description @@ -4765,15 +4675,15 @@ annotation infrastructure.") `((upstream-name . "topGO"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-sparsem" ,r-sparsem))) + (list r-annotationdbi + r-dbi + r-biobase + r-biocgenerics + r-go-db + r-graph + r-lattice + r-matrixstats + r-sparsem)) (home-page "https://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") (description @@ -4796,7 +4706,7 @@ dependencies between GO terms can be implemented and applied.") "0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description @@ -4821,24 +4731,24 @@ of gene-level counts.") (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biostrings + r-bsgenome + r-dbi + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrixgenerics + r-summarizedexperiment + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector + r-zlibbioc)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") @@ -4859,13 +4769,9 @@ coding changes and predict coding outcomes.") "03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-ggplot2" ,r-ggplot2) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma))) + (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description @@ -4895,14 +4801,14 @@ and specific in detecting differential transcription.") (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs - `(("r-alluvial" ,r-alluvial) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-mclust" ,r-mclust) - ("r-plyr" ,r-plyr) - ("r-stringdb" ,r-stringdb))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-alluvial + r-ggplot2 + r-gridextra + r-igraph + r-mclust + r-plyr + r-stringdb)) + (native-inputs (list r-knitr)) (home-page "https://git.bioconductor.org/packages/XINA") (synopsis "Identifying proteins that exhibit similar patterns") (description @@ -4969,11 +4875,9 @@ describing each of the graphs.") (("import\\(zlibbioc\\)") "")) #t))))) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-iranges r-s4vectors)) (home-page "https://bioconductor.org/packages/XVector") (synopsis "Representation and manpulation of external sequences") (description @@ -5013,15 +4917,15 @@ libraries for systems that do not have these available via other means.") (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk" ,r-basilisk) - ("r-cli" ,r-cli) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-reticulate" ,r-reticulate) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk + r-cli + r-delayedarray + r-matrix + r-reticulate + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://github.com/theislab/zellkonverter") (synopsis "Conversion between AnnData and single-cell experiments objects") (description @@ -5045,12 +4949,12 @@ saving AnnData objects to disk.") "1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-lattice" ,r-lattice) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-lattice + r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/geneplotter") (synopsis "Graphics functions for genomic data") (description @@ -5071,19 +4975,19 @@ saving AnnData objects to disk.") (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs - `(("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-affyio + r-biobase + r-biocgenerics + r-biocmanager + r-biostrings + r-dbi + r-ff + r-foreach + r-genomicranges + r-iranges + r-rsqlite + r-s4vectors + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/oligoClasses/") (synopsis "Classes for high-throughput arrays") (description @@ -5105,21 +5009,21 @@ packages.") "1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-affxparser" ,r-affxparser) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-ff" ,r-ff) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite) - ("r-zlibbioc" ,r-zlibbioc))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-affxparser + r-affyio + r-biobase + r-biocgenerics + r-biostrings + r-dbi + r-ff + r-oligoclasses + r-preprocesscore + r-rsqlite + r-zlibbioc)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/oligo/") (synopsis "Preprocessing tools for oligonucleotide arrays") (description @@ -5141,10 +5045,9 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") "1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138")))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-reshape2" ,r-reshape2))) + (list r-ggplot2 r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description @@ -5196,13 +5099,13 @@ integration with @code{Rcpp}.") (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs - `(("r-emdbook" ,r-emdbook) - ("r-genomicranges" ,r-genomicranges) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcppnumerical" ,r-rcppnumerical) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-emdbook + r-genomicranges + r-rcpp + r-rcppeigen + r-rcppnumerical + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for @@ -5223,14 +5126,14 @@ posterior for individual coefficients.") (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-mass" ,r-mass) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-mass + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high @@ -5251,29 +5154,29 @@ signal in the input, that lead to spurious peaks during peak calling.") (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apeglm" ,r-apeglm) - ("r-ashr" ,r-ashr) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gplots" ,r-gplots) - ("r-greylistchip" ,r-greylistchip) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcolorbrewer" , r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-systempiper" ,r-systempiper))) + (list r-amap + r-apeglm + r-ashr + r-biocparallel + r-deseq2 + r-dplyr + r-genomicalignments + r-genomicranges + r-ggplot2 + r-ggrepel + r-gplots + r-greylistchip + r-iranges + r-lattice + r-limma + r-locfit + r-rcolorbrewer + r-rcpp + r-rhtslib + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-systempiper)) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description @@ -5296,13 +5199,13 @@ occupancy (overlap) analysis and plotting functions.") (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rsamtools" ,r-rsamtools) - ("r-genomicalignments" ,r-genomicalignments) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-s4vectors + r-iranges + r-genomicranges + r-summarizedexperiment + r-rsamtools + r-genomicalignments + r-rtracklayer)) (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") @@ -5327,20 +5230,20 @@ processing to visualization and annotation.") "03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-benchmarkme" ,r-benchmarkme) - ("r-biocparallel" ,r-biocparallel) - ("r-clusterr" ,r-clusterr) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-knitr)) + (propagated-inputs + (list r-beachmat + r-benchmarkme + r-biocparallel + r-clusterr + r-delayedarray + r-matrix + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/mbkmeans") (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") (description "This package implements the mini-batch k-means algorithm for @@ -5360,10 +5263,7 @@ large datasets, including support for on-disk data representation.") "03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns")))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-survival r-biocgenerics r-biobase r-mass)) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description @@ -5397,7 +5297,7 @@ expressed genes in DNA microarray experiments.") "0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description @@ -5419,8 +5319,7 @@ expressed genes in DNA microarray experiments.") (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-igraph" ,r-igraph))) + (list r-graph r-igraph)) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description @@ -5443,9 +5342,7 @@ fitting of some classes of graphical Markov models.") (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-limma" ,r-limma) - ("r-rbgl" ,r-rbgl))) + (list r-graph r-limma r-rbgl)) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description @@ -5469,9 +5366,7 @@ a given recall, F-score for single and multiple classes are available.") (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) + (list r-codetools r-graph r-xml)) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description @@ -5497,33 +5392,33 @@ determining dependencies between variables, code improvement suggestions.") (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-matrixstats" ,r-matrixstats) - ("r-multtest" ,r-multtest) - ("r-rbgl" ,r-rbgl) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biomart + r-biostrings + r-dbi + r-dplyr + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-graph + r-interactionset + r-iranges + r-keggrest + r-matrixstats + r-multtest + r-rbgl + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description @@ -5551,7 +5446,7 @@ enrichedGO (addGeneIDs).") `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs - `(("r-matrixstats" ,r-matrixstats))) + (list r-matrixstats)) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description @@ -5575,7 +5470,7 @@ incompatibilities.") (base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz")))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma))) + (list r-limma)) (home-page "https://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted @@ -5595,8 +5490,7 @@ normalization and quality checking.") (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-marray" ,r-marray))) + (list r-biobase r-marray)) (home-page "https://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5615,11 +5509,7 @@ the @code{arrayCGH} packages.") (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-impute" ,r-impute) - ("r-dnacopy" ,r-dnacopy) - ("r-snowfall" ,r-snowfall))) + (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall)) (home-page "https://bioconductor.org/packages/CGHcall") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by @@ -5638,16 +5528,16 @@ the @code{arrayCGH} packages.") (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cghbase" ,r-cghbase) - ("r-cghcall" ,r-cghcall) - ("r-dnacopy" ,r-dnacopy) - ("r-future-apply" ,r-future-apply) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-r-utils" ,r-r-utils) - ("r-rsamtools" ,r-rsamtools))) + (list r-biobase + r-cghbase + r-cghcall + r-dnacopy + r-future-apply + r-genomicranges + r-iranges + r-matrixstats + r-r-utils + r-rsamtools)) (home-page "https://bioconductor.org/packages/QDNAseq") (synopsis "Quantitative DNA sequencing for chromosomal aberrations") (description "The genome is divided into non-overlapping fixed-sized bins, @@ -5672,9 +5562,7 @@ respectively.") (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-edger" ,r-edger) - ("r-genomicranges" ,r-genomicranges))) + (list r-abind r-edger r-genomicranges)) (home-page "https://bioconductor.org/packages/baySeq/") (synopsis "Bayesian analysis of differential expression patterns in count data") (description @@ -5698,16 +5586,16 @@ more complex hypotheses) via empirical Bayesian methods.") (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics + r-bsgenome-hsapiens-ucsc-hg19 + r-bsgenome-mmusculus-ucsc-mm9 + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rsamtools + r-rtracklayer + r-s4vectors)) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description @@ -5732,24 +5620,24 @@ datasets.") (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sqldf" ,r-sqldf))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-data-table + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-plyr + r-reshape2 + r-rsamtools + r-rtracklayer + r-s4vectors + r-sqldf)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/RiboProfiling/") (synopsis "Ribosome profiling data analysis") (description "Starting with a BAM file, this package provides the @@ -5773,13 +5661,13 @@ assessment, principal component analysis on codon coverage.") (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-bayseq" ,r-bayseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-seqlogo" ,r-seqlogo))) + (list r-abind + r-bayseq + r-genomeinfodb + r-genomicranges + r-iranges + r-rsamtools + r-seqlogo)) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description @@ -5802,16 +5690,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.") `((upstream-name . "InteractionSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/InteractionSet") (synopsis "Base classes for storing genomic interaction data") (description @@ -5836,24 +5724,24 @@ experiments.") `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-interactionset" ,r-interactionset) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gridextra + r-gviz + r-igraph + r-interactionset + r-iranges + r-rsamtools + r-rtracklayer + r-s4vectors + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") (synopsis "R package for handling genomic interaction data") (description @@ -5874,7 +5762,7 @@ information and producing various plots and statistics.") (base32 "1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx")))) (build-system r-build-system) - (propagated-inputs `(("r-amap" ,r-amap))) + (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") (synopsis "Cluster and tree conversion") (description @@ -5895,12 +5783,12 @@ trees and clusters to other programs.") "1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biasedurn" ,r-biasedurn) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genelendatabase" ,r-genelendatabase) - ("r-go-db" ,r-go-db) - ("r-mgcv" ,r-mgcv))) + (list r-annotationdbi + r-biasedurn + r-biocgenerics + r-genelendatabase + r-go-db + r-mgcv)) (home-page "https://bioconductor.org/packages/goseq/") (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") (description @@ -5922,15 +5810,15 @@ defined categories which are over/under represented in RNA-seq data.") (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-edger" ,r-edger) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jsonlite" ,r-jsonlite) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-deseq2 + r-edger + r-htmlwidgets + r-jsonlite + r-limma + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -5955,8 +5843,7 @@ information.") (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-rcpp)) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description @@ -5978,8 +5865,7 @@ in omics data.") "06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-mass" ,r-mass))) + (list r-biobase r-mass)) (home-page "http://www.genopolis.it") (synopsis "Detect differential expression in microarray and proteomics datasets") (description @@ -6004,30 +5890,29 @@ genes or proteins in these datasets.") (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-deseq2" ,r-deseq2) - ("r-desolve" ,r-desolve) - ("r-gdata" ,r-gdata) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-plgem" ,r-plgem) - ("r-proc" ,r-proc) - ("r-rootsolve" ,r-rootsolve) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-txdb-mmusculus-ucsc-mm9-knowngene" - ,r-txdb-mmusculus-ucsc-mm9-knowngene))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-deseq2 + r-desolve + r-gdata + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-kernsmooth + r-plgem + r-proc + r-rootsolve + r-rsamtools + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment + r-txdb-mmusculus-ucsc-mm9-knowngene)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/INSPEcT") (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") (description @@ -6051,11 +5936,9 @@ modeling the rates that determines changes in mature mRNA levels.") (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description @@ -6080,12 +5963,9 @@ demultiplexed, i.e. assigned to their original reference barcode.") (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edaseq" ,r-edaseq) - ("r-edger" ,r-edger) - ("r-mass" ,r-mass))) + (list r-biobase r-edaseq r-edger r-mass)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description @@ -6108,13 +5988,9 @@ samples.") (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description @@ -6140,10 +6016,8 @@ achieved for all methods using the BiocParallel framework.") (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-delayedarray r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/LTLA/ScaledMatrix") (synopsis "Create a DelayedMatrix of scaled and centered values") (description @@ -6168,14 +6042,14 @@ multiplication.") (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-dplyr" ,r-dplyr) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rlang" ,r-rlang) - ("r-tibble" ,r-tibble) - ("r-tidytree" ,r-tidytree))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-dplyr + r-jsonlite + r-magrittr + r-rlang + r-tibble + r-tidytree)) + (native-inputs (list r-knitr)) (home-page "https://github.com/YuLab-SMU/treeio") (synopsis "Base classes and functions for Phylogenetic tree input and output") (description @@ -6200,20 +6074,20 @@ platform for merging tree with associated data and converting file formats.") (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs - `(("r-ape" ,r-ape) - ("r-aplot" ,r-aplot) - ("r-dplyr" ,r-dplyr) - ("r-ggfun" ,r-ggfun) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-purrr" ,r-purrr) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales) - ("r-tidyr" ,r-tidyr) - ("r-tidytree" ,r-tidytree) - ("r-treeio" ,r-treeio) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-ape + r-aplot + r-dplyr + r-ggfun + r-ggplot2 + r-magrittr + r-purrr + r-rlang + r-scales + r-tidyr + r-tidytree + r-treeio + r-yulab-utils)) + (native-inputs (list r-knitr)) (home-page "https://yulab-smu.top/treedata-book/") (synopsis "R package for visualization of trees and annotation data") (description @@ -6237,9 +6111,9 @@ data.") (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + (list r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/metapod") (synopsis "Meta-analyses on p-values of differential analyses") (description @@ -6266,18 +6140,18 @@ missing values and weighting where appropriate.") (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-irlba" ,r-irlba) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rsvd" ,r-rsvd) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-irlba + r-matrix + r-rcpp + r-rsvd + r-s4vectors + r-scaledmatrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/BiocSingular") (synopsis "Singular value decomposition for Bioconductor packages") (description @@ -6300,30 +6174,30 @@ possible, parallelization is achieved using the BiocParallel framework.") "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-ggplot-multistats" ,r-ggplot-multistats) - ("r-ggplot2" ,r-ggplot2) - ("r-ggthemes" ,r-ggthemes) - ("r-irlba" ,r-irlba) - ("r-knn-covertree" ,r-knn-covertree) - ("r-matrix" ,r-matrix) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-rcpphnsw" ,r-rcpphnsw) - ("r-rspectra" ,r-rspectra) - ("r-scales" ,r-scales) - ("r-scatterplot3d" ,r-scatterplot3d) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-smoother" ,r-smoother) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-vim" ,r-vim))) - (native-inputs - `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes + (list r-biobase + r-biocgenerics + r-ggplot-multistats + r-ggplot2 + r-ggthemes + r-irlba + r-knn-covertree + r-matrix + r-pcamethods + r-proxy + r-rcpp + r-rcppeigen + r-rcpphnsw + r-rspectra + r-scales + r-scatterplot3d + r-singlecellexperiment + r-smoother + r-summarizedexperiment + r-tidyr + r-tidyselect + r-vim)) + (native-inputs + (list r-nbconvertr)) ; for vignettes (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -6345,11 +6219,7 @@ maps.") (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) + (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml)) (home-page "https://github.com/bcalder/savR") (synopsis "Parse and analyze Illumina SAV files") (description @@ -6371,25 +6241,25 @@ Viewer (SAV) files, access data, and generate QC plots.") (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biovizbase" ,r-biovizbase) - ("r-broom" ,r-broom) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hexbin" ,r-hexbin) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-biovizbase + r-broom + r-data-table + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-hexbin + r-iranges + r-rcolorbrewer + r-rmarkdown + r-rsamtools + r-s4vectors + r-scales + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/keleslab/ChIPexoQual") (synopsis "Quality control pipeline for ChIP-exo/nexus data") (description @@ -6409,10 +6279,7 @@ sequencing data.") "143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534")))) (build-system r-build-system) (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-s4vectors r-iranges r-genomicranges r-biocgenerics)) (home-page "https://bioconductor.org/packages/copynumber") (synopsis "Segmentation of single- and multi-track copy number data") (description @@ -6433,7 +6300,7 @@ penalized least squares regression method.") "19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/DNAcopy") (synopsis "DNA copy number data analysis") (description @@ -6458,9 +6325,7 @@ abnormal copy number.") (properties `((upstream-name . "HTSCluster"))) (build-system r-build-system) (propagated-inputs - `(("r-capushe" ,r-capushe) - ("r-edger" ,r-edger) - ("r-plotrix" ,r-plotrix))) + (list r-capushe r-edger r-plotrix)) (home-page "https://cran.r-project.org/web/packages/HTSCluster") (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") (description @@ -6512,7 +6377,7 @@ and summarizing a set of statistics using a weighted distance approach.") (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-qvalue" ,r-qvalue))) + (list r-qvalue)) (home-page "https://cran.r-project.org/web/packages/NBPSeq") (synopsis "Negative binomial models for RNA-Seq data") (description @@ -6534,9 +6399,7 @@ and regression inferences from RNA-sequencing data.") (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-blockmodeling" ,r-blockmodeling) - ("r-gplots" ,r-gplots) - ("r-testthat" ,r-testthat))) + (list r-blockmodeling r-gplots r-testthat)) (home-page "https://bioconductor.org/packages/EBSeq") (synopsis "Differential expression analysis of RNA-seq data") (description @@ -6556,23 +6419,23 @@ gene and isoform level using RNA-seq data") "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-bamsignals" ,r-bamsignals) - ("r-bezier" ,r-bezier) - ("r-biovizbase" ,r-biovizbase) - ("r-digest" ,r-digest) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-memoise" ,r-memoise) - ("r-regioner" ,r-regioner) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-bamsignals + r-bezier + r-biovizbase + r-digest + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-memoise + r-regioner + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/karyoploteR/") (synopsis "Plot customizable linear genomes displaying arbitrary data") (description "This package creates karyotype plots of arbitrary genomes and @@ -6595,10 +6458,9 @@ coordinates.") "1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description @@ -6626,12 +6488,9 @@ to install interface to SYMPHONY.") (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-fdrtool" ,r-fdrtool) - ("r-lpsymphony" ,r-lpsymphony) - ("r-slam" ,r-slam))) + (list r-biocgenerics r-fdrtool r-lpsymphony r-slam)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description @@ -6658,19 +6517,19 @@ independent of the p-value under the null hypothesis.") (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-limma" ,r-limma) - ("r-reshape2" ,r-reshape2) - ("r-rocr" ,r-rocr) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-shinydashboard" ,r-shinydashboard) - ("r-upsetr" ,r-upsetr))) + (list r-dplyr + r-dt + r-ggplot2 + r-limma + r-reshape2 + r-rocr + r-scales + r-shiny + r-shinybs + r-shinydashboard + r-upsetr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/iCOBRA") (synopsis "Comparison and visualization of ranking and assignment methods") (description @@ -6695,11 +6554,9 @@ interactive exploration of results.") `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors))) + (list r-delayedarray r-matrix r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LTLA/ResidualMatrix") (synopsis "Create a DelayedMatrix of regression residuals") (description @@ -6725,23 +6582,23 @@ multiplication and calculation of row/column sums or means.") (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-residualmatrix" ,r-residualmatrix) - ("r-s4vectors" ,r-s4vectors) - ("r-scaledmatrix" ,r-scaledmatrix) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-igraph + r-matrix + r-rcpp + r-residualmatrix + r-s4vectors + r-scaledmatrix + r-scuttle + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/batchelor") (synopsis "Single-Cell Batch Correction Methods") (description @@ -6768,20 +6625,20 @@ the numbers of cells across batches.") (properties `((upstream-name . "MAST"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-abind + r-biobase + r-biocgenerics + r-data-table + r-ggplot2 + r-plyr + r-progress + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-stringr + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/MAST/") (synopsis "Model-based analysis of single cell transcriptomics") (description @@ -6802,38 +6659,38 @@ single cell assay data.") "0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocviews" ,r-biocviews) - ("r-cluster" ,r-cluster) - ("r-combinat" ,r-combinat) - ("r-ddrtree" ,r-ddrtree) - ("r-densityclust" ,r-densityclust) - ("r-dplyr" ,r-dplyr) - ("r-fastica" ,r-fastica) - ("r-ggplot2" ,r-ggplot2) - ("r-hsmmsinglecell" ,r-hsmmsinglecell) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-proxy" ,r-proxy) - ("r-qlcmatrix" ,r-qlcmatrix) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-slam" ,r-slam) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-vgam" ,r-vgam) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocviews + r-cluster + r-combinat + r-ddrtree + r-densityclust + r-dplyr + r-fastica + r-ggplot2 + r-hsmmsinglecell + r-igraph + r-irlba + r-limma + r-mass + r-matrix + r-matrixstats + r-pheatmap + r-plyr + r-proxy + r-qlcmatrix + r-rann + r-rcpp + r-reshape2 + r-rtsne + r-slam + r-stringr + r-tibble + r-vgam + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/monocle") (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") (description @@ -6865,11 +6722,11 @@ qPCR data, but could be used with other types as well.") (properties `((upstream-name . "leidenbase"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (native-inputs - `(("gfortran" ,gfortran))) + (list gfortran)) (propagated-inputs - `(("r-igraph" ,r-igraph))) + (list r-igraph)) (home-page "https://github.com/cole-trapnell-lab/leidenbase") (synopsis "R and C wrappers to run the Leiden find_partition function") (description @@ -6898,11 +6755,7 @@ several functions from the R igraph package.") "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) (build-system r-build-system) (propagated-inputs - `(("r-generics" ,r-generics) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo))) + (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://pneuvial.github.io/sanssouci") (synopsis "Post Hoc multiple testing inference") (description @@ -6927,50 +6780,50 @@ user-defined and/or data-driven sets of hypotheses.") "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-batchelor" ,r-batchelor) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-grr" ,r-grr) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-igraph" ,r-igraph) - ("r-irlba" ,r-irlba) - ("r-leidenbase" ,r-leidenbase) - ("r-limma" ,r-limma) - ("r-lmtest" ,r-lmtest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrix-utils" ,r-matrix-utils) - ("r-pbapply" ,r-pbapply) - ("r-pbmcapply" ,r-pbmcapply) - ("r-pheatmap" ,r-pheatmap) - ("r-plotly" ,r-plotly) - ("r-pryr" ,r-pryr) - ("r-proxy" ,r-proxy) - ("r-pscl" ,r-pscl) - ("r-purrr" ,r-purrr) - ("r-rann" ,r-rann) - ("r-rcpp" ,r-rcpp) - ("r-rcppparallel" ,r-rcppparallel) - ("r-reshape2" ,r-reshape2) - ("r-reticulate" ,r-reticulate) - ("r-rhpcblasctl" ,r-rhpcblasctl) - ("r-rsample" ,r-rsample) - ("r-rtsne" ,r-rtsne) - ("r-shiny" ,r-shiny) - ("r-slam" ,r-slam) - ("r-spdep" ,r-spdep) - ("r-speedglm" ,r-speedglm) - ("r-stringr" ,r-stringr) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-uwot" ,r-uwot) - ("r-viridis" ,r-viridis))) + (list r-assertthat + r-batchelor + r-biobase + r-biocgenerics + r-delayedmatrixstats + r-dplyr + r-ggplot2 + r-ggrepel + r-grr + r-htmlwidgets + r-igraph + r-irlba + r-leidenbase + r-limma + r-lmtest + r-mass + r-matrix + r-matrix-utils + r-pbapply + r-pbmcapply + r-pheatmap + r-plotly + r-pryr + r-proxy + r-pscl + r-purrr + r-rann + r-rcpp + r-rcppparallel + r-reshape2 + r-reticulate + r-rhpcblasctl + r-rsample + r-rtsne + r-shiny + r-slam + r-spdep + r-speedglm + r-stringr + r-singlecellexperiment + r-tibble + r-tidyr + r-uwot + r-viridis)) (home-page "https://github.com/cole-trapnell-lab/monocle3") (synopsis "Analysis toolkit for single-cell RNA-Seq data") (description @@ -6991,8 +6844,7 @@ user-defined and/or data-driven sets of hypotheses.") (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-matrix" ,r-matrix))) + (list r-biobase r-matrix)) (home-page "https://bioconductor.org/packages/NOISeq") (synopsis "Exploratory analysis and differential expression for RNA-seq data") (description @@ -7018,19 +6870,19 @@ assumptions.") (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs - `(("r-arm" ,r-arm) - ("r-biocparallel" ,r-biocparallel) - ("r-ebseq" ,r-ebseq) - ("r-fields" ,r-fields) - ("r-ggplot2" ,r-ggplot2) - ("r-mclust" ,r-mclust) - ("r-outliers" ,r-outliers) - ("r-s4vectors" ,r-s4vectors) - ("r-scran" ,r-scran) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-arm + r-biocparallel + r-ebseq + r-fields + r-ggplot2 + r-mclust + r-outliers + r-s4vectors + r-scran + r-singlecellexperiment + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description @@ -7055,29 +6907,29 @@ distributions.") "1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1")))) (build-system r-build-system) (propagated-inputs - `(("r-aroma-light" ,r-aroma-light) - ("r-biocparallel" ,r-biocparallel) - ("r-boot" ,r-boot) - ("r-class" ,r-class) - ("r-cluster" ,r-cluster) - ("r-compositions" ,r-compositions) - ("r-diptest" ,r-diptest) - ("r-edger" ,r-edger) - ("r-fpc" ,r-fpc) - ("r-gplots" ,r-gplots) - ("r-hexbin" ,r-hexbin) - ("r-limma" ,r-limma) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-mixtools" ,r-mixtools) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rhdf5" ,r-rhdf5) - ("r-ruvseq" ,r-ruvseq) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aroma-light + r-biocparallel + r-boot + r-class + r-cluster + r-compositions + r-diptest + r-edger + r-fpc + r-gplots + r-hexbin + r-limma + r-matrixgenerics + r-matrixstats + r-mixtools + r-rarpack + r-rcolorbrewer + r-rhdf5 + r-ruvseq + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description @@ -7100,18 +6952,18 @@ high-throughput analyses.") (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-tidyr" ,r-tidyr) - ("r-xml2" ,r-xml2))) + (list r-biobase + r-data-table + r-dplyr + r-httr + r-limma + r-magrittr + r-r-utils + r-readr + r-tidyr + r-xml2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description @@ -7134,7 +6986,7 @@ the bridge between GEO and BioConductor.") "0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m")))) (build-system r-build-system) (propagated-inputs - `(("r-base64" ,r-base64))) + (list r-base64)) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description @@ -7155,9 +7007,7 @@ files, including IDAT.") "1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multtest" ,r-multtest) - ("r-scrime" ,r-scrime))) + (list r-biobase r-multtest r-scrime)) (home-page "https://bioconductor.org/packages/siggenes/") (synopsis "Multiple testing using SAM and Efron's empirical Bayes approaches") @@ -7181,19 +7031,19 @@ Bayes Analyses of Microarrays} (EBAM).") "0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dorng" ,r-dorng) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationdbi + r-biocgenerics + r-dorng + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-iterators + r-limma + r-locfit + r-matrixstats + r-s4vectors)) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description @@ -7215,37 +7065,37 @@ studies.") "0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx")))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bumphunter" ,r-bumphunter) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-geoquery" ,r-geoquery) - ("r-hdf5array" ,r-hdf5array) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-nlme" ,r-nlme) - ("r-nor1mix" ,r-nor1mix) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quadprog" ,r-quadprog) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-s4vectors" ,r-s4vectors) - ("r-siggenes" ,r-siggenes) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bumphunter + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genefilter + r-genomeinfodb + r-genomicranges + r-geoquery + r-hdf5array + r-illuminaio + r-iranges + r-lattice + r-limma + r-mass + r-mclust + r-nlme + r-nor1mix + r-preprocesscore + r-quadprog + r-rcolorbrewer + r-reshape + r-s4vectors + r-siggenes + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description @@ -7266,27 +7116,27 @@ methylation arrays.") "1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka")))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) - ("r-genefilter" ,r-genefilter) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-illuminaio" ,r-illuminaio) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-matrixstats" ,r-matrixstats) - ("r-minfi" ,r-minfi) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotate + r-annotationdbi + r-biobase + r-biocgenerics + r-fdb-infiniummethylation-hg19 + r-genefilter + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-illuminaio + r-iranges + r-lattice + r-matrixstats + r-minfi + r-reshape2 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description @@ -7313,21 +7163,21 @@ and Infinium HD arrays are also included.") "0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-dbi" ,r-dbi) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-methylumi" ,r-methylumi) - ("r-mgcv" ,r-mgcv) - ("r-nleqslv" ,r-nleqslv) - ("r-preprocesscore" ,r-preprocesscore) - ("r-rsqlite" ,r-rsqlite))) + (list r-affy + r-annotate + r-annotationdbi + r-biobase + r-dbi + r-genomicfeatures + r-genomicranges + r-kernsmooth + r-lattice + r-mass + r-methylumi + r-mgcv + r-nleqslv + r-preprocesscore + r-rsqlite)) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description @@ -7353,26 +7203,26 @@ especially Illumina Infinium methylation microarrays.") (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs - `(("r-amap" ,r-amap) - ("r-apcluster" ,r-apcluster) - ("r-ellipse" ,r-ellipse) - ("r-fastcluster" ,r-fastcluster) - ("r-fpc" ,r-fpc) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass) - ("r-mclust" ,r-mclust) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rtsne" ,r-rtsne) - ("r-statmod" ,r-statmod) - ("r-vegan" ,r-vegan) - ("r-zoo" ,r-zoo))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-amap + r-apcluster + r-ellipse + r-fastcluster + r-fpc + r-ggdendro + r-ggplot2 + r-gmodels + r-igraph + r-limma + r-mass + r-mclust + r-rcpp + r-rcpparmadillo + r-rtsne + r-statmod + r-vegan + r-zoo)) + (native-inputs + (list r-knitr)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description @@ -7414,21 +7264,21 @@ evaluation of DEG analysis methods.") (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bit64" ,r-bit64) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-rhdf5" ,r-rhdf5) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bit64 + r-dplyr + r-ggplot2 + r-magrittr + r-rhdf5 + r-shortread + r-stringr + r-tibble + r-tidyr + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description @@ -7455,10 +7305,7 @@ surface of a flowcell.") (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs - `(("r-multcomp" ,r-multcomp) - ("r-multtest" ,r-multtest) - ("r-mvtnorm" ,r-mvtnorm) - ("r-plotrix" ,r-plotrix))) + (list r-multcomp r-multtest r-mvtnorm r-plotrix)) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description @@ -7483,10 +7330,7 @@ are standardized and usable by the accompanying mutossGUI package.") "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs - `(("r-lattice" ,r-lattice) - ("r-mutoss" ,r-mutoss) - ("r-rdpack" ,r-rdpack) - ("r-tfisher" ,r-tfisher))) + (list r-lattice r-mutoss r-rdpack r-tfisher)) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description @@ -7509,28 +7353,28 @@ published results; and a routine for graphical display.") "1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mgcv" ,r-mgcv) - ("r-pbapply" ,r-pbapply) - ("r-princurve" ,r-princurve) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-slingshot" ,r-slingshot) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-trajectoryutils" ,r-trajectoryutils) - ("r-viridis" ,r-viridis))) + (list r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-igraph + r-magrittr + r-mass + r-matrix + r-matrixstats + r-mgcv + r-pbapply + r-princurve + r-rcolorbrewer + r-s4vectors + r-singlecellexperiment + r-slingshot + r-summarizedexperiment + r-tibble + r-trajectoryutils + r-viridis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://statomics.github.io/tradeSeq/index.html") (synopsis "Trajectory-based differential expression analysis") (description @@ -7557,9 +7401,7 @@ performs inference on the parameters of the GAM.") "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-yaml" ,r-yaml))) + (list r-biocgenerics r-iranges r-yaml)) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description @@ -7582,20 +7424,20 @@ peak definition in combination with known profile characteristics.") (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-matrix + r-rsamtools + r-rtracklayer + r-s4vectors + r-variantannotation)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description @@ -7622,7 +7464,7 @@ gmapR.") (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs - `(("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-rcolorbrewer)) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description @@ -7647,11 +7489,9 @@ information about samples and features can be added to the plot.") (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-go-db" ,r-go-db) - ("r-rcpp" ,r-rcpp))) + (list r-annotationdbi r-go-db r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description @@ -7675,8 +7515,7 @@ sets of GO terms, gene products and gene clusters.") "0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f")))) (build-system r-build-system) (propagated-inputs - `(("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue))) + (list r-multtest r-qvalue)) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description @@ -7728,15 +7567,15 @@ phenotype of interest.") (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs - `(("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-plyr" ,r-plyr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-doparallel + r-foreach + r-genomicranges + r-iranges + r-plyr + r-rtracklayer + r-summarizedexperiment + r-variantannotation)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/fcScan") (synopsis "Detect clusters of coordinates with user defined options") (description @@ -7761,16 +7600,16 @@ presence of additional sites within the allowed window size.") "10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-fastmatch" ,r-fastmatch) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-bh + r-biocparallel + r-data-table + r-fastmatch + r-ggplot2 + r-gridextra + r-matrix + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description @@ -7794,16 +7633,16 @@ to multiple hypothesis correction.") (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocparallel" ,r-biocparallel) - ("r-do-db" ,r-do-db) - ("r-fgsea" ,r-fgsea) - ("r-ggplot2" ,r-ggplot2) - ("r-gosemsim" ,r-gosemsim) - ("r-qvalue" ,r-qvalue) - ("r-reshape2" ,r-reshape2))) + (list r-annotationdbi + r-biocparallel + r-do-db + r-fgsea + r-ggplot2 + r-gosemsim + r-qvalue + r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description @@ -7828,23 +7667,23 @@ data.") "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) (build-system r-build-system) (propagated-inputs - `(("r-aplot" ,r-aplot) - ("r-dose" ,r-dose) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-ggtree" ,r-ggtree) - ("r-gosemsim" ,r-gosemsim) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-scatterpie" ,r-scatterpie) - ("r-shadowtext" ,r-shadowtext) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aplot + r-dose + r-ggplot2 + r-ggraph + r-ggtree + r-gosemsim + r-igraph + r-magrittr + r-plyr + r-purrr + r-rcolorbrewer + r-reshape2 + r-scatterpie + r-shadowtext + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description @@ -7868,21 +7707,21 @@ All the visualization methods are developed based on ggplot2 graphics.") `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-downloader" ,r-downloader) - ("r-dplyr" ,r-dplyr) - ("r-enrichplot" ,r-enrichplot) - ("r-go-db" ,r-go-db) - ("r-gosemsim" ,r-gosemsim) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-qvalue" ,r-qvalue) - ("r-rlang" ,r-rlang) - ("r-tidyr" ,r-tidyr) - ("r-yulab-utils" ,r-yulab-utils))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-dose + r-downloader + r-dplyr + r-enrichplot + r-go-db + r-gosemsim + r-magrittr + r-plyr + r-qvalue + r-rlang + r-tidyr + r-yulab-utils)) + (native-inputs + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description @@ -7902,33 +7741,33 @@ profiles (GO and KEGG) of gene and gene clusters.") "0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc")))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-ape" ,r-ape) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocsingular" ,r-biocsingular) - ("r-cluster" ,r-cluster) - ("r-delayedarray" ,r-delayedarray) - ("r-edger" ,r-edger) - ("r-hdf5array" ,r-hdf5array) - ("r-howmany" ,r-howmany) - ("r-kernlab" ,r-kernlab) - ("r-limma" ,r-limma) - ("r-locfdr" ,r-locfdr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mbkmeans" ,r-mbkmeans) - ("r-nmf" ,r-nmf) - ("r-phylobase" ,r-phylobase) - ("r-pracma" ,r-pracma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-zinbwave" ,r-zinbwave))) + (list r-knitr)) + (propagated-inputs + (list r-ape + r-biocgenerics + r-biocsingular + r-cluster + r-delayedarray + r-edger + r-hdf5array + r-howmany + r-kernlab + r-limma + r-locfdr + r-matrix + r-matrixstats + r-mbkmeans + r-nmf + r-phylobase + r-pracma + r-rcolorbrewer + r-rcpp + r-s4vectors + r-scales + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-zinbwave)) (home-page "https://bioconductor.org/packages/clusterExperiment/") (synopsis "Compare clusterings for single-cell sequencing") (description "This package provides functionality for running and comparing @@ -7950,26 +7789,26 @@ expression data sets.") (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fpc" ,r-fpc) - ("r-gbm" ,r-gbm) - ("r-gdata" ,r-gdata) - ("r-genefilter" ,r-genefilter) - ("r-ggvis" ,r-ggvis) - ("r-hwriter" ,r-hwriter) - ("r-magrittr" ,r-magrittr) - ("r-mass" ,r-mass) - ("r-mlbench" ,r-mlbench) - ("r-pls" ,r-pls) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rpart" ,r-rpart) - ("r-sfsmisc" ,r-sfsmisc) - ("r-shiny" ,r-shiny) - ("r-threejs" ,r-threejs))) + (list r-annotate + r-biobase + r-biocgenerics + r-cluster + r-fpc + r-gbm + r-gdata + r-genefilter + r-ggvis + r-hwriter + r-magrittr + r-mass + r-mlbench + r-pls + r-rcolorbrewer + r-rcpp + r-rpart + r-sfsmisc + r-shiny + r-threejs)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description @@ -7998,11 +7837,7 @@ data in R and Bioconductor containers.") (substitute* "DESCRIPTION" ((", KEGG.db") ""))))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-dbi" ,r-dbi) - ("r-go-db" ,r-go-db))) + (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db)) (home-page "https://bioconductor.org/packages/annaffy/") (synopsis "Annotation tools for Affymetrix biological metadata") (description @@ -8028,10 +7863,9 @@ It allows searching of biological metadata using various criteria.") (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet))) + (list r-biobase r-glmnet)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Core") (synopsis "Automated Affymetrix array analysis core package") (description @@ -8053,15 +7887,15 @@ arrays.") (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-biobase" ,r-biobase) - ("r-glmnet" ,r-glmnet) - ("r-pamr" ,r-pamr) - ("r-rocr" ,r-rocr) - ("r-varselrf" ,r-varselrf))) + (list r-a4core + r-a4preproc + r-biobase + r-glmnet + r-pamr + r-rocr + r-varselrf)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Classif/") (synopsis "Automated Affymetrix array analysis classification package") (description @@ -8083,10 +7917,9 @@ Affymetrix arrays.") (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics))) + (list r-biobase r-biocgenerics)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Preproc/") (synopsis "Automated Affymetrix array analysis preprocessing package") (description @@ -8108,9 +7941,9 @@ is used for preprocessing the arrays.") (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs - `(("r-xtable" ,r-xtable))) + (list r-xtable)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/a4Reporting/") (synopsis "Automated Affymetrix array analysis reporting package") (description @@ -8132,16 +7965,16 @@ provides reporting features.") (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs - `(("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-genefilter" ,r-genefilter) - ("r-glmnet" ,r-glmnet) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-mpm" ,r-mpm) - ("r-multtest" ,r-multtest))) + (list r-a4core + r-a4preproc + r-annaffy + r-biobase + r-genefilter + r-glmnet + r-gplots + r-limma + r-mpm + r-multtest)) (home-page "https://bioconductor.org/packages/a4Base/") (synopsis "Automated Affymetrix array analysis base package") (description @@ -8162,11 +7995,7 @@ Affymetrix arrays.") "0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m")))) (build-system r-build-system) (propagated-inputs - `(("r-a4base" ,r-a4base) - ("r-a4classif" ,r-a4classif) - ("r-a4core" ,r-a4core) - ("r-a4preproc" ,r-a4preproc) - ("r-a4reporting" ,r-a4reporting))) + (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) (home-page "https://bioconductor.org/packages/a4/") (synopsis "Automated Affymetrix array analysis umbrella package") (description @@ -8188,28 +8017,28 @@ Affymetrix arrays.") (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs - `(("pandoc" ,pandoc))) - (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-circlize" ,r-circlize) - ("r-flexdashboard" ,r-flexdashboard) - ("r-ggcorrplot" ,r-ggcorrplot) - ("r-ggdendro" ,r-ggdendro) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-knitr" ,r-knitr) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-png" ,r-png) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rmarkdown" ,r-rmarkdown) - ("r-stringr" ,r-stringr) - ("r-vegan" ,r-vegan) - ("r-venndiagram" ,r-venndiagram))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list pandoc)) + (propagated-inputs + (list r-biocparallel + r-biocstyle + r-circlize + r-flexdashboard + r-ggcorrplot + r-ggdendro + r-ggplot2 + r-gridextra + r-knitr + r-plotly + r-plyr + r-png + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-stringr + r-vegan + r-venndiagram)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/malhamdoosh/abseqR") (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") (description @@ -8235,11 +8064,9 @@ further downstream analysis on its output.") "13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-ellipse" ,r-ellipse) - ("r-ggplot2" ,r-ggplot2))) + (list r-biocparallel r-ellipse r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/bacon/") (synopsis "Controlling bias and inflation in association studies") (description @@ -8263,11 +8090,7 @@ fitting a three-component normal mixture on z-scores.") (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-seqlogo" ,r-seqlogo))) + (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo)) (home-page "https://bioconductor.org/packages/rGADEM/") (synopsis "De novo sequence motif discovery") (description @@ -8289,15 +8112,15 @@ genomic sequence data.") (properties `((upstream-name . "MotIV"))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-rgadem" ,r-rgadem) - ("r-s4vectors" ,r-s4vectors))) + (list gsl)) + (propagated-inputs + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-lattice + r-rgadem + r-s4vectors)) (home-page "https://bioconductor.org/packages/MotIV/") (synopsis "Motif identification and validation") (description @@ -8319,15 +8142,15 @@ distributions, modules and filter motifs.") (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-splitstackshape" ,r-splitstackshape))) + (list r-biocgenerics + r-biostrings + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-splitstackshape)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -8346,26 +8169,26 @@ frequency matrices from nine public sources, for multiple organisms.") (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-grimport" ,r-grimport) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-matrixstats" ,r-matrixstats) - ("r-motifdb" ,r-motifdb) - ("r-motifstack" ,r-motifstack) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-grimport + r-gviz + r-iranges + r-matrixstats + r-motifdb + r-motifstack + r-rtracklayer + r-s4vectors + r-stringr + r-summarizedexperiment + r-tfmpvalue + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/motifbreakR/") (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") (description "This package allows biologists to judge in the first place @@ -8399,13 +8222,9 @@ Bioconductor.") (properties `((upstream-name . "motifStack"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-xml" ,r-xml))) + (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -8430,22 +8249,22 @@ type and symbol colors.") (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biobase" ,r-biobase) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-delayedarray" ,r-delayedarray) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biobase + r-biocfilecache + r-biocgenerics + r-biocmanager + r-biostrings + r-delayedarray + r-genomeinfodb + r-genomicranges + r-hdf5array + r-iranges + r-rhdf5 + r-s4vectors + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description @@ -8467,26 +8286,26 @@ position-specific scores within R and Bioconductor.") (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-chippeakanno" ,r-chippeakanno) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-iranges" ,r-iranges) - ("r-kernsmooth" ,r-kernsmooth) - ("r-limma" ,r-limma) - ("r-motifstack" ,r-motifstack) - ("r-preseqr" ,r-preseqr) - ("r-randomforest" ,r-randomforest) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-bsgenome + r-chippeakanno + r-edger + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-genomicscores + r-iranges + r-kernsmooth + r-limma + r-motifstack + r-preseqr + r-randomforest + r-rsamtools + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/ATACseqQC/") (synopsis "ATAC-seq quality control") (description @@ -8514,15 +8333,15 @@ footprints.") (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-mapplots" ,r-mapplots) - ("r-rcpp" ,r-rcpp) - ("r-vioplot" ,r-vioplot))) + (list r-annotationdbi + r-genomicranges + r-gtools + r-iranges + r-mapplots + r-rcpp + r-vioplot)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description @@ -8563,14 +8382,14 @@ annotations and ontologies.") (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs - `(("r-abadata" ,r-abadata) - ("r-data-table" ,r-data-table) - ("r-gofuncr" ,r-gofuncr) - ("r-gplots" ,r-gplots) - ("r-gtools" ,r-gtools) - ("r-rcpp" ,r-rcpp))) + (list r-abadata + r-data-table + r-gofuncr + r-gplots + r-gtools + r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description @@ -8596,8 +8415,7 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.") `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dbi" ,r-dbi))) + (list r-annotationdbi r-dbi)) (home-page "https://www.iysik.com/r/annotationfuncs") (synopsis "Annotation translation functions") (description @@ -8620,7 +8438,7 @@ different identifieres using the Biocore Data Team data-packages (e.g. (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/annotationTools/") (synopsis "Annotate microarrays and perform gene expression analyses") (description @@ -8646,27 +8464,27 @@ text files).") `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-gridextra" ,r-gridextra) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-nlme" ,r-nlme) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-gridextra + r-gviz + r-iranges + r-lattice + r-latticeextra + r-nlme + r-rsamtools + r-s4vectors + r-seqinr + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description @@ -8688,16 +8506,16 @@ investigation using RNA-seq data.") (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-gseabase" ,r-gseabase) - ("r-mixtools" ,r-mixtools) - ("r-r-utils" ,r-r-utils) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-gseabase + r-mixtools + r-r-utils + r-s4vectors + r-shiny + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description @@ -8727,18 +8545,18 @@ needed.") (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocgenerics" ,r-biocgenerics) - ("r-fftwtools" ,r-fftwtools) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-jpeg" ,r-jpeg) - ("r-locfit" ,r-locfit) - ("r-png" ,r-png) - ("r-rcurl" ,r-rcurl) - ("r-tiff" ,r-tiff))) + (list r-abind + r-biocgenerics + r-fftwtools + r-htmltools + r-htmlwidgets + r-jpeg + r-locfit + r-png + r-rcurl + r-tiff)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://github.com/aoles/EBImage") (synopsis "Image processing and analysis toolbox for R") (description @@ -8765,18 +8583,17 @@ visualization with image data.") "141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-ebimage" ,r-ebimage) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-mzr" ,r-mzr) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" - ,r-summarizedexperiment))) + (list r-biocgenerics + r-data-table + r-ebimage + r-iranges + r-limma + r-matrix + r-mzr + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description @@ -8799,12 +8616,9 @@ analysis.") "0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl")))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges))) + (list r-circlize r-genomicranges r-getoptlong r-iranges)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description @@ -8830,21 +8644,21 @@ genomic categories and to add self-defined graphics in the plot.") `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-nmf" ,r-nmf) - ("r-pcamethods" ,r-pcamethods) - ("r-proxy" ,r-proxy) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-genomeinfodb + r-genomicranges + r-ggbio + r-ggplot2 + r-iranges + r-nmf + r-pcamethods + r-proxy + r-reshape2 + r-s4vectors + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description @@ -8868,31 +8682,31 @@ decomposition algorithms.") (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-corrplot" ,r-corrplot) - ("r-dendextend" ,r-dendextend) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtrellis" ,r-gtrellis) - ("r-keggrest" ,r-keggrest) - ("r-limsolve" ,r-limsolve) - ("r-magrittr" ,r-magrittr) - ("r-pmcmr" ,r-pmcmr) - ("r-pracma" ,r-pracma) - ("r-reshape2" ,r-reshape2) - ("r-somaticsignatures" ,r-somaticsignatures) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome-hsapiens-ucsc-hg19 + r-circlize + r-complexheatmap + r-corrplot + r-dendextend + r-doparallel + r-dplyr + r-genomeinfodb + r-genomicranges + r-getoptlong + r-ggbeeswarm + r-ggplot2 + r-gridextra + r-gtrellis + r-keggrest + r-limsolve + r-magrittr + r-pmcmr + r-pracma + r-reshape2 + r-somaticsignatures + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description @@ -8916,12 +8730,12 @@ provided.") "0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-affyio" ,r-affyio) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-biostrings" ,r-biostrings) - ("r-xvector" ,r-xvector))) + (list r-affy + r-affyio + r-biobase + r-biocmanager + r-biostrings + r-xvector)) (home-page "https://bioconductor.org/packages/gcrma/") (synopsis "Background adjustment using sequence information") (description @@ -8952,11 +8766,7 @@ gene-specific binding is expected.") "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gcrma" ,r-gcrma) - ("r-genefilter" ,r-genefilter))) + (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter)) (home-page "https://bioconductor.org/packages/simpleaffy/") (synopsis "Very simple high level analysis of Affymetrix data") (description @@ -8980,7 +8790,7 @@ generating high resolution journal figures.") "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (build-system r-build-system) (propagated-inputs - `(("r-simpleaffy" ,r-simpleaffy))) + (list r-simpleaffy)) (home-page "https://bioconductor.org/packages/yaqcaffy/") (synopsis "Affymetrix quality control and reproducibility analysis") (description @@ -9002,15 +8812,15 @@ chips with the MAQC reference datasets.") "1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-iterators" ,r-iterators) - ("r-minfi" ,r-minfi) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-doparallel + r-foreach + r-ggplot2 + r-iterators + r-minfi + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description @@ -9035,19 +8845,19 @@ groups.") "0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biomart" ,r-biomart) - ("r-downloader" ,r-downloader) - ("r-edger" ,r-edger) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore) - ("r-quantro" ,r-quantro) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-readr" ,r-readr))) + (list r-biobase + r-biomart + r-downloader + r-edger + r-gplots + r-limma + r-matrixstats + r-preprocesscore + r-quantro + r-rcolorbrewer + r-readr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description @@ -9072,14 +8882,14 @@ large RNA-seq experiments.") "0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description @@ -9102,17 +8912,17 @@ sites and alignments obtained from standard RNA-seq experiments.") (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-locfit" ,r-locfit) - ("r-magrittr" ,r-magrittr) - ("r-matrixstats" ,r-matrixstats) - ("r-pracma" ,r-pracma) - ("r-roar" ,r-roar))) + (list r-biobase + r-deseq2 + r-dplyr + r-ggplot2 + r-locfit + r-magrittr + r-matrixstats + r-pracma + r-roar)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description @@ -9142,7 +8952,7 @@ genes.") `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) (propagated-inputs - `(("r-waveslim" ,r-waveslim))) + (list r-waveslim)) (home-page "https://bioconductor.org/packages/MassSpecWavelet/") (synopsis "Mass spectrum processing by wavelet-based algorithms") (description @@ -9164,25 +8974,25 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-massspecwavelet" ,r-massspecwavelet) - ("r-mscoreutils" ,r-mscoreutils) - ("r-msfeatures" ,r-msfeatures) - ("r-msnbase" ,r-msnbase) - ("r-mzr" ,r-mzr) - ("r-plyr" ,r-plyr) - ("r-protgenerics" ,r-protgenerics) - ("r-rann" ,r-rann) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-robustbase" ,r-robustbase) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-iranges + r-lattice + r-massspecwavelet + r-mscoreutils + r-msfeatures + r-msnbase + r-mzr + r-plyr + r-protgenerics + r-rann + r-rcolorbrewer + r-robustbase + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/xcms/") (synopsis "LC/MS and GC/MS mass spectrometry data analysis") (description @@ -9206,11 +9016,9 @@ data for high-throughput, untargeted analyte profiling.") (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats))) + (list r-limma r-locfit r-matrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description @@ -9231,18 +9039,18 @@ that arising from 16s metagenomic surveys.") "01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-cowplot" ,r-cowplot) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-purrr" ,r-purrr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-assertthat + r-cowplot + r-dplyr + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-purrr + r-rtracklayer + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description @@ -9286,17 +9094,16 @@ widgets in R.") "1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17")))) (build-system r-build-system) (inputs - `(("netpbm" ,netpbm) - ("perl" ,perl))) - (propagated-inputs - `(("r-affy" ,r-affy) - ("r-annaffy" ,r-annaffy) - ("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-gcrma" ,r-gcrma) - ("r-multtest" ,r-multtest) - ("r-qvalue" ,r-qvalue) - ("r-vsn" ,r-vsn))) + (list netpbm perl)) + (propagated-inputs + (list r-affy + r-annaffy + r-biobase + r-biocmanager + r-gcrma + r-multtest + r-qvalue + r-vsn)) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description @@ -9319,15 +9126,15 @@ Currently only Affymetrix oligonucleotide analysis is supported.") "05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq")))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-edger" ,r-edger) - ("r-genefilter" ,r-genefilter) - ("r-matrix" ,r-matrix) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-softimpute" ,r-softimpute) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocparallel + r-edger + r-genefilter + r-matrix + r-singlecellexperiment + r-softimpute + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/zinbwave") (synopsis "Zero-inflated negative binomial model for RNA-seq data") (description "This package implements a general and flexible zero-inflated @@ -9353,13 +9160,9 @@ the data.") (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description @@ -9382,13 +9185,11 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs - `(("r-magrittr" ,r-magrittr) - ("r-rsamtools" ,r-rsamtools))) + (list r-magrittr r-rsamtools)) (inputs - `(("samtools" ,samtools) - ("zlib" ,zlib))) + (list samtools zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description @@ -9410,14 +9211,14 @@ rapid adapter trimming, identification, and read merging.") "0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-dplyr" ,r-dplyr) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-dplyr + r-ggplot2 + r-ggrepel + r-gridextra + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description @@ -9441,7 +9242,7 @@ expression\".") (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) - (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) + (propagated-inputs (list r-arrmdata)) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description @@ -9464,16 +9265,16 @@ Infinium HumanMethylation 450k assay.") (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-dbi" ,r-dbi) - ("r-dbplyr" ,r-dbplyr) - ("r-dplyr" ,r-dplyr) - ("r-filelock" ,r-filelock) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs) - ("r-rsqlite" ,r-rsqlite))) + (list r-curl + r-dbi + r-dbplyr + r-dplyr + r-filelock + r-httr + r-rappdirs + r-rsqlite)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description @@ -9496,7 +9297,7 @@ and data files used across sessions.") "0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) - (native-inputs `(("gfortran" ,gfortran))) + (native-inputs (list gfortran)) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description @@ -9527,7 +9328,7 @@ Gaussian distributions.") (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description @@ -9550,22 +9351,22 @@ alignment tool.") (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-runit" ,r-runit) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biocgenerics + r-biostrings + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-igraph + r-iranges + r-rsamtools + r-rtracklayer + r-runit + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/SGSeq/") (synopsis "Splice event prediction and quantification from RNA-seq data") (description @@ -9605,11 +9406,9 @@ interpretation.") (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-sgseq" ,r-sgseq))) + (list r-genomicfeatures r-genomicranges r-sgseq)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description @@ -9633,25 +9432,25 @@ index.") (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rbowtie" ,r-rbowtie) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-iranges + r-rbowtie + r-rhtslib + r-rsamtools + r-rtracklayer + r-s4vectors + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description @@ -9675,26 +9474,26 @@ quantification of genomic regions of interest.") (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocstyle" ,r-biocstyle) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-plyr" ,r-plyr) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shortread" ,r-shortread))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biocstyle + r-biostrings + r-biovizbase + r-genomicalignments + r-genomicfiles + r-ggplot2 + r-iranges + r-knitr + r-markdown + r-plyr + r-rcpp + r-reshape2 + r-rsamtools + r-s4vectors + r-shiny + r-shortread)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description @@ -9718,10 +9517,7 @@ graphics.") (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs - `(("r-igraph" ,r-igraph) - ("r-matrix" ,r-matrix) - ("r-slam" ,r-slam) - ("r-tsne" ,r-tsne))) + (list r-igraph r-matrix r-slam r-tsne)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -9746,9 +9542,7 @@ routines to analyse the resulting networks and their natural projections.") "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limma" ,r-limma) - ("r-mass" ,r-mass))) + (list r-biobase r-limma r-mass)) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description @@ -9776,18 +9570,18 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-qqman" ,r-qqman) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-ggrepel + r-iranges + r-limma + r-qqman + r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description @@ -9812,10 +9606,9 @@ packages.") "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-multidataset" ,r-multidataset))) + (list r-biobase r-multidataset)) (native-inputs - `(("r-knitr" ,r-knitr))) ; for vignettes + (list r-knitr)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description @@ -9850,13 +9643,9 @@ coefficients).") "189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-multidataset" ,r-multidataset) - ("r-randomforest" ,r-randomforest) - ("r-ropls" ,r-ropls))) + (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description @@ -9883,21 +9672,21 @@ datasets.") "1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-dplyr" ,r-dplyr) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-regioner" ,r-regioner) - ("r-reshape2" ,r-reshape2) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-iranges + r-readr + r-regioner + r-reshape2 + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description @@ -9924,9 +9713,9 @@ annotations.") "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-matrix" ,r-matrix))) + (list r-matrix)) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description @@ -9951,12 +9740,12 @@ and to both short and long sequence reads.") (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-flowcore" ,r-flowcore) - ("r-graph" ,r-graph) - ("r-runit" ,r-runit) - ("r-xml" ,r-xml))) + (list r-biobase + r-corpcor + r-flowcore + r-graph + r-runit + r-xml)) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description @@ -9978,9 +9767,7 @@ and to both short and long sequence reads.") `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs - `(("r-all" ,r-all) - ("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster))) + (list r-all r-biobase r-cluster)) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description @@ -10002,14 +9789,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib))) + (list r-bh + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rhdf5lib + r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description @@ -10031,17 +9818,17 @@ interact with gated cytometry data.") (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors))) + (list r-bh + r-biobase + r-biocgenerics + r-cytolib + r-matrixstats + r-rcpp + r-rcpparmadillo + r-rprotobuflib + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description @@ -10063,10 +9850,7 @@ with flow cytometry data.") (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-feature" ,r-feature) - ("r-flowcore" ,r-flowcore) - ("r-rrcov" ,r-rrcov))) + (list r-biobase r-feature r-flowcore r-rrcov)) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description @@ -10089,16 +9873,16 @@ change point detection.") (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-flowcore" ,r-flowcore) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-bh + r-biobase + r-biocgenerics + r-flowcore + r-rcpp + r-rcpparmadillo + r-rhdf5lib + r-zlibbioc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description @@ -10120,19 +9904,19 @@ manipulation of flow cytometry data.") (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) + (list r-data-table + r-flowcore + r-flowworkspace + r-ggplot2 + r-gridextra + r-hexbin + r-ncdfflow + r-plyr + r-rcolorbrewer + r-rlang + r-scales)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description @@ -10157,17 +9941,17 @@ statistics to the plot.") (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-flowcore" ,r-flowcore) - ("r-hexbin" ,r-hexbin) - ("r-idpmisc" ,r-idpmisc) - ("r-kernsmooth" ,r-kernsmooth) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-mass" ,r-mass) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-biobase + r-flowcore + r-hexbin + r-idpmisc + r-kernsmooth + r-lattice + r-latticeextra + r-mass + r-rcolorbrewer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description @@ -10191,20 +9975,19 @@ statistics to the plot.") `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-corpcor" ,r-corpcor) - ("r-ellipse" ,r-ellipse) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-graph" ,r-graph) - ("r-mnormt" ,r-mnormt))) + (list r-biobase + r-biocgenerics + r-clue + r-corpcor + r-ellipse + r-flowcore + r-flowviz + r-graph + r-mnormt)) (inputs - `(("gsl" ,gsl))) + (list gsl)) (native-inputs - `(("pkg-config" ,pkg-config) - ("r-knitr" ,r-knitr))) + (list pkg-config r-knitr)) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description @@ -10235,7 +10018,7 @@ model with Box-Cox transformation.") (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.13.0.tar.gz"))))))) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description @@ -10257,35 +10040,35 @@ for other R packages to compile and link against.") (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs - `(("r-aws-s3" ,r-aws-s3) - ("r-aws-signature" ,r-aws-signature) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-ggplot2" ,r-ggplot2) - ("r-graph" ,r-graph) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-aws-s3 + r-aws-signature + r-bh + r-biobase + r-biocgenerics + r-cytolib + r-data-table + r-delayedarray + r-digest + r-dplyr + r-flowcore + r-ggplot2 + r-graph + r-lattice + r-latticeextra + r-matrixstats + r-ncdfflow + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-s4vectors + r-scales + r-xml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description @@ -10311,20 +10094,20 @@ matches the flowJo analysis.") (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-cluster" ,r-cluster) - ("r-fda" ,r-fda) - ("r-flowcore" ,r-flowcore) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-kernsmooth" ,r-kernsmooth) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rrcov" ,r-rrcov))) + (list r-biobase + r-biocgenerics + r-cluster + r-fda + r-flowcore + r-flowviz + r-flowworkspace + r-kernsmooth + r-ks + r-lattice + r-mass + r-ncdfflow + r-rcolorbrewer + r-rrcov)) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description @@ -10347,29 +10130,29 @@ package.") (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-clue" ,r-clue) - ("r-data-table" ,r-data-table) - ("r-flowclust" ,r-flowclust) - ("r-flowcore" ,r-flowcore) - ("r-flowstats" ,r-flowstats) - ("r-flowviz" ,r-flowviz) - ("r-flowworkspace" ,r-flowworkspace) - ("r-graph" ,r-graph) - ("r-gtools" ,r-gtools) - ("r-ks" ,r-ks) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-ncdfflow" ,r-ncdfflow) - ("r-plyr" ,r-plyr) - ("r-r-utils" ,r-r-utils) - ("r-rbgl" ,r-rbgl) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rrcov" ,r-rrcov))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-clue + r-data-table + r-flowclust + r-flowcore + r-flowstats + r-flowviz + r-flowworkspace + r-graph + r-gtools + r-ks + r-lattice + r-mass + r-ncdfflow + r-plyr + r-r-utils + r-rbgl + r-rcolorbrewer + r-rcpp + r-rrcov)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description @@ -10391,38 +10174,37 @@ sequential way to mimic the manual gating strategy.") (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs - `(("libxml2" ,libxml2) - ("zlib" ,zlib))) - (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biobase" ,r-biobase) - ("r-corpcor" ,r-corpcor) - ("r-cytolib" ,r-cytolib) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggcyto" ,r-ggcyto) - ("r-graph" ,r-graph) - ("r-jsonlite" ,r-jsonlite) - ("r-lattice" ,r-lattice) - ("r-opencyto" ,r-opencyto) - ("r-plyr" ,r-plyr) - ("r-rbgl" ,r-rbgl) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rcppparallel" ,r-rcppparallel) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-rprotobuflib" ,r-rprotobuflib) - ("r-runit" ,r-runit) - ("r-tibble" ,r-tibble) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list libxml2 zlib)) + (propagated-inputs + (list r-base64enc + r-bh + r-biobase + r-corpcor + r-cytolib + r-data-table + r-dplyr + r-flowcore + r-flowworkspace + r-ggcyto + r-graph + r-jsonlite + r-lattice + r-opencyto + r-plyr + r-rbgl + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-rgraphviz + r-rhdf5lib + r-rprotobuflib + r-runit + r-tibble + r-xml + r-xml2 + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description @@ -10444,28 +10226,28 @@ standard to exchange gated cytometry data with other software platforms.") (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-colorramps" ,r-colorramps) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cytoml" ,r-cytoml) - ("r-dplyr" ,r-dplyr) - ("r-flowcore" ,r-flowcore) - ("r-flowworkspace" ,r-flowworkspace) - ("r-ggforce" ,r-ggforce) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpointdensity" ,r-ggpointdensity) - ("r-ggpubr" ,r-ggpubr) - ("r-ggrepel" ,r-ggrepel) - ("r-igraph" ,r-igraph) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-scattermore" ,r-scattermore) - ("r-tidyr" ,r-tidyr) - ("r-xml" ,r-xml))) + (list r-biocgenerics + r-colorramps + r-consensusclusterplus + r-cytoml + r-dplyr + r-flowcore + r-flowworkspace + r-ggforce + r-ggnewscale + r-ggplot2 + r-ggpointdensity + r-ggpubr + r-ggrepel + r-igraph + r-magrittr + r-pheatmap + r-rcolorbrewer + r-rlang + r-rtsne + r-scattermore + r-tidyr + r-xml)) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description @@ -10487,23 +10269,23 @@ self-organizing map clustering and minimal spanning trees.") (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-corpcor" ,r-corpcor) - ("r-dplyr" ,r-dplyr) - ("r-ellipse" ,r-ellipse) - ("r-ggrepel" ,r-ggrepel) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-igraph" ,r-igraph) - ("r-lattice" ,r-lattice) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-rarpack" ,r-rarpack) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-corpcor + r-dplyr + r-ellipse + r-ggrepel + r-ggplot2 + r-gridextra + r-igraph + r-lattice + r-mass + r-matrixstats + r-rarpack + r-rcolorbrewer + r-reshape2 + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description @@ -10533,25 +10315,25 @@ delete entire rows with missing data.") (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs - `(("r-beanplot" ,r-beanplot) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gmodels" ,r-gmodels) - ("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats) - ("r-mixomics" ,r-mixomics) - ("r-moments" ,r-moments) - ("r-rcpp" ,r-rcpp) - ("r-rcppeigen" ,r-rcppeigen) - ("r-reshape2" ,r-reshape2) - ("r-robustbase" ,r-robustbase) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beanplot + r-dosnow + r-dplyr + r-fnn + r-foreach + r-ggplot2 + r-gmodels + r-gplots + r-mass + r-matrixstats + r-mixomics + r-moments + r-rcpp + r-rcppeigen + r-reshape2 + r-robustbase + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description @@ -10579,20 +10361,20 @@ data, to only emphasize the data that actually matters.") (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs - `(("r-arrow" ,r-arrow) - ("r-aucell" ,r-aucell) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-feather" ,r-feather) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gseabase" ,r-gseabase) - ("r-r-utils" ,r-r-utils) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-arrow + r-aucell + r-biocgenerics + r-data-table + r-dplyr + r-feather + r-genomeinfodb + r-genomicranges + r-gseabase + r-r-utils + r-summarizedexperiment + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description @@ -10621,12 +10403,8 @@ genes in the gene-set that are ranked above the leading edge).") (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-delaporte" ,r-delaporte) - ("r-hmisc" ,r-hmisc) - ("r-mass" ,r-mass) - ("r-matrixstats" ,r-matrixstats))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description @@ -10646,30 +10424,30 @@ genes in the gene-set that are ranked above the leading edge).") "1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7")))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-fnn" ,r-fnn) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-glasso" ,r-glasso) - ("r-gviz" ,r-gviz) - ("r-igraph" ,r-igraph) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-monocle" ,r-monocle) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vgam" ,r-vgam))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biobase + r-biocgenerics + r-data-table + r-dplyr + r-fnn + r-genomicranges + r-ggplot2 + r-glasso + r-gviz + r-igraph + r-iranges + r-matrix + r-monocle + r-plyr + r-reshape2 + r-s4vectors + r-stringi + r-stringr + r-tibble + r-tidyr + r-vgam)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description @@ -10696,9 +10474,9 @@ accessibility data.") (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs - `(("r-monocle3" ,r-monocle3) - ,@(alist-delete "r-monocle" - (package-propagated-inputs r-cicero))))))) + (modify-inputs (package-propagated-inputs r-cicero) + (delete "r-monocle") + (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package @@ -10715,31 +10493,31 @@ accessibility data.") `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-edger" ,r-edger) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-gwascat" ,r-gwascat) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringi" ,r-stringi) - ("r-stringr" ,r-stringr) - ("r-universalmotif" ,r-universalmotif))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-deseq2 + r-dplyr + r-edger + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gwascat + r-iranges + r-magrittr + r-r-utils + r-readr + r-reshape2 + r-rlang + r-rtracklayer + r-s4vectors + r-seqinr + r-stringi + r-stringr + r-universalmotif)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis @@ -10769,21 +10547,21 @@ analysis, evolutionary conservation, biogenesis to functional analysis.") "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-dosnow" ,r-dosnow) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-aucell + r-data-table + r-dplyr + r-dosnow + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description @@ -10816,24 +10594,24 @@ cisTopics and explore the nature and regulatory proteins driving them.") "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . "cisTopic"))) (propagated-inputs - `(("r-aucell" ,r-aucell) - ("r-data-table" ,r-data-table) - ("r-dosnow" ,r-dosnow) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-feather" ,r-feather) - ("r-fitdistrplus" ,r-fitdistrplus) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-lda" ,r-lda) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rcistarget" ,r-rcistarget) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-text2vec" ,r-text2vec))) + (list r-aucell + r-data-table + r-dosnow + r-dplyr + r-dt + r-feather + r-fitdistrplus + r-genomicranges + r-ggplot2 + r-lda + r-matrix + r-plyr + r-rcistarget + r-rtracklayer + r-s4vectors + r-text2vec)) (native-inputs - `(("r-knitr" ,r-knitr)))))) + (list r-knitr))))) (define-public r-genie3 (package @@ -10849,10 +10627,9 @@ cisTopics and explore the nature and regulatory proteins driving them.") (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs - `(("r-dplyr" ,r-dplyr) - ("r-reshape2" ,r-reshape2))) + (list r-dplyr r-reshape2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description @@ -10874,7 +10651,7 @@ regulatory networks from expression data.") (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description @@ -10899,7 +10676,7 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") `((upstream-name . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) (build-system r-build-system) - (propagated-inputs `(("r-minfi" ,r-minfi))) + (propagated-inputs (list r-minfi)) (home-page "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") (synopsis "Annotation for Illumina's 450k methylation arrays") @@ -10922,17 +10699,16 @@ data.") (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-illuminahumanmethylation450kanno-ilmn12-hg19" - ,r-illuminahumanmethylation450kanno-ilmn12-hg19) - ("r-illuminaio" ,r-illuminaio) - ("r-limma" ,r-limma) - ("r-lumi" ,r-lumi) - ("r-matrixstats" ,r-matrixstats) - ("r-methylumi" ,r-methylumi) - ("r-roc" ,r-roc))) + (list r-biobase + r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminaio + r-limma + r-lumi + r-matrixstats + r-methylumi + r-roc)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description @@ -10983,11 +10759,9 @@ metrics, with methods for objects produced by the @code{methylumi} and (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs - `(("lz4" ,lz4) - ("xz" ,xz) - ("zlib" ,zlib))) + (list lz4 xz zlib)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") @@ -11019,14 +10793,14 @@ with multiple R processes supported by the package @code{parallel}.") (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-gdsfmt" ,r-gdsfmt) - ("r-geoquery" ,r-geoquery) - ("r-illuminaio" ,r-illuminaio) - ("r-methylumi" ,r-methylumi) - ("r-minfi" ,r-minfi) - ("r-watermelon" ,r-watermelon))) + (list r-biobase + r-biocgenerics + r-gdsfmt + r-geoquery + r-illuminaio + r-methylumi + r-minfi + r-watermelon)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -11048,9 +10822,7 @@ with multiple R processes supported by the package @code{parallel}.") (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib))) + (list r-biostrings r-genomicranges r-rhtslib)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description @@ -11076,13 +10848,13 @@ genome sequence.") ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-bsgenome" ,r-bsgenome) - ("r-biostrings" ,r-biostrings))) + (list r-biocgenerics + r-s4vectors + r-iranges + r-genomeinfodb + r-genomicranges + r-bsgenome + r-biostrings)) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") @@ -11112,9 +10884,7 @@ injected in that sequence).") (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs - `(("r-rjava" ,r-rjava) - ("r-rsamtools" ,r-rsamtools) - ("r-seqbias" ,r-seqbias))) + (list r-rjava r-rsamtools r-seqbias)) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description @@ -11137,22 +10907,22 @@ format.") (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-foreach" ,r-foreach) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-mclust" ,r-mclust) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqinr" ,r-seqinr) - ("r-stringr" ,r-stringr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-foreach + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-hmisc + r-iranges + r-mclust + r-rsamtools + r-rtracklayer + r-s4vectors + r-seqinr + r-stringr)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/wavClusteR/") (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") (description @@ -11185,23 +10955,23 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") `((upstream-name . "TimeSeriesExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-deseq2" ,r-deseq2) - ("r-dplyr" ,r-dplyr) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-edger" ,r-edger) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-proxy" ,r-proxy) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-vegan" ,r-vegan) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-deseq2 + r-dplyr + r-dynamictreecut + r-edger + r-ggplot2 + r-hmisc + r-limma + r-magrittr + r-proxy + r-s4vectors + r-summarizedexperiment + r-tibble + r-tidyr + r-vegan + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description @@ -11226,30 +10996,30 @@ provides methods for retrieving enriched pathways.") `((upstream-name . "VariantFiltering"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-genomicscores" ,r-genomicscores) - ("r-graph" ,r-graph) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-rbgl" ,r-rbgl) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-shinyjs" ,r-shinyjs) - ("r-shinythemes" ,r-shinythemes) - ("r-shinytree" ,r-shinytree) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation) - ("r-xvector" ,r-xvector))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-genomicscores + r-graph + r-gviz + r-iranges + r-rbgl + r-rsamtools + r-s4vectors + r-shiny + r-shinyjs + r-shinythemes + r-shinytree + r-summarizedexperiment + r-variantannotation + r-xvector)) (home-page "https://github.com/rcastelo/VariantFiltering") (synopsis "Filtering of coding and non-coding genetic variants") (description @@ -11272,7 +11042,7 @@ populations, splice site strength, conservation, etc.") (properties `((upstream-name . "GenomeGraphs"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart))) + (list r-biomart)) (home-page "https://bioconductor.org/packages/GenomeGraphs/") (synopsis "Plotting genomic information from Ensembl") (description @@ -11300,16 +11070,16 @@ same genome coordinate system.") (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-genomegraphs" ,r-genomegraphs) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-oligo" ,r-oligo) - ("r-oligoclasses" ,r-oligoclasses) - ("r-preprocesscore" ,r-preprocesscore) - ("r-waveslim" ,r-waveslim))) + (list r-affy + r-biobase + r-biostrings + r-genomegraphs + r-genomicranges + r-iranges + r-oligo + r-oligoclasses + r-preprocesscore + r-waveslim)) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description @@ -11332,25 +11102,25 @@ arrays based on fast wavelet-based functional models.") `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocparallel" ,r-biocparallel) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-gplots" ,r-gplots) - ("r-iterators" ,r-iterators) - ("r-limma" ,r-limma) - ("r-lme4" ,r-lme4) - ("r-lmertest" ,r-lmertest) - ("r-mass" ,r-mass) - ("r-matrix" ,r-matrix) - ("r-pbkrtest" ,r-pbkrtest) - ("r-progress" ,r-progress) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-scales" ,r-scales))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocparallel + r-doparallel + r-foreach + r-ggplot2 + r-gplots + r-iterators + r-limma + r-lme4 + r-lmertest + r-mass + r-matrix + r-pbkrtest + r-progress + r-reshape2 + r-rlang + r-scales)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/variancePartition/") (synopsis "Analyze variation in gene expression experiments") (description @@ -11376,11 +11146,7 @@ measures.") (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gplots" ,r-gplots) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer)) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") @@ -11411,8 +11177,7 @@ features (e.g. genes, microRNAs).") `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-htqpcr" ,r-htqpcr))) + (list r-biocgenerics r-htqpcr)) (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") (description @@ -11443,18 +11208,18 @@ data.") (substitute* "src/Makevars" (("/usr/bin/strip") (which "strip")))))))) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-rcppthread" ,r-rcppthread) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biostrings + r-ggplot2 + r-iranges + r-mass + r-rcpp + r-rcppthread + r-rlang + r-s4vectors + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/universalmotif/") (synopsis @@ -11486,15 +11251,15 @@ motifs, and others.") `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) + (list r-biostrings + r-bsgenome + r-bsgenome-hsapiens-ucsc-hg19 + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description @@ -11521,10 +11286,9 @@ using whole genome sequencing data.") `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-ggplot2" ,r-ggplot2))) + (list r-data-table r-ggplot2)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description @@ -11549,7 +11313,7 @@ cellular organization in health and disease.") (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs - `(("r-kernsmooth" ,r-kernsmooth))) + (list r-kernsmooth)) (home-page "https://bioconductor.org/packages/BGmix/") (synopsis "Bayesian models for differential gene expression") (description @@ -11571,10 +11335,7 @@ gene expression.") (properties `((upstream-name . "bgx"))) (build-system r-build-system) (propagated-inputs - `(("r-affy" ,r-affy) - ("r-biobase" ,r-biobase) - ("r-gcrma" ,r-gcrma) - ("r-rcpp" ,r-rcpp))) + (list r-affy r-biobase r-gcrma r-rcpp)) (home-page "https://bioconductor.org/packages/bgx/") (synopsis "Bayesian gene expression") (description @@ -11622,9 +11383,7 @@ algorithm which is more efficient for larger data sets.") (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-gseabase" ,r-gseabase) - ("r-multtest" ,r-multtest))) + (list r-biobase r-gseabase r-multtest)) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description @@ -11646,10 +11405,9 @@ results.") (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-poibin" ,r-poibin))) + (list r-genomicranges r-poibin)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description @@ -11676,12 +11434,11 @@ the read count and GC content bias.") (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs - `(("libsbml" ,libsbml))) + (list libsbml)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph))) + (list r-biocgenerics r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "http://www.sbml.org") (synopsis "R support for SBML") (description @@ -11703,7 +11460,7 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (home-page "https://bioconductor.org/packages/hypergraph") (synopsis "Hypergraph data structures") (description @@ -11724,11 +11481,9 @@ manipulating hypergraphs.") "1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) - (inputs `(("graphviz" ,graphviz))) + (inputs (list graphviz)) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-hypergraph" ,r-hypergraph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-graph r-hypergraph r-rgraphviz)) (home-page "https://bioconductor.org/packages/hyperdraw") (synopsis "Visualizing hypergraphs") (description @@ -11749,12 +11504,12 @@ manipulating hypergraphs.") (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs - `(("r-hyperdraw" ,r-hyperdraw) - ("r-hypergraph" ,r-hypergraph) - ("r-lim" ,r-lim) - ("r-limsolve" ,r-limsolve) - ("r-rsbml" ,r-rsbml) - ("r-stringr" ,r-stringr))) + (list r-hyperdraw + r-hypergraph + r-lim + r-limsolve + r-rsbml + r-stringr)) (home-page "https://bioconductor.org/packages/BiGGR/") (synopsis "Constraint based modeling using metabolic reconstruction databases") (description @@ -11780,9 +11535,9 @@ networks and estimated fluxes can be visualized with hypergraphs.") `((upstream-name . "bigmemoryExtras"))) (build-system r-build-system) (propagated-inputs - `(("r-bigmemory" ,r-bigmemory))) + (list r-bigmemory)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/phaverty/bigmemoryExtras") (synopsis "Extension of the bigmemory package") (description @@ -11813,26 +11568,26 @@ a file-backed matrix with factor properties.") (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-dplyr" ,r-dplyr) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-hexbin" ,r-hexbin) - ("r-hmisc" ,r-hmisc) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-plotly" ,r-plotly) - ("r-plyr" ,r-plyr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape" ,r-reshape) - ("r-shiny" ,r-shiny) - ("r-shinycssloaders" ,r-shinycssloaders) - ("r-shinydashboard" ,r-shinydashboard) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-delayedarray + r-dplyr + r-ggally + r-ggplot2 + r-gridextra + r-hexbin + r-hmisc + r-htmlwidgets + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-shiny + r-shinycssloaders + r-shinydashboard + r-stringr + r-summarizedexperiment + r-tidyr)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/lindsayrutter/bigPint") (synopsis "Big multivariate data plotted interactively") (description @@ -11856,23 +11611,23 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs - `(("r-base64enc" ,r-base64enc) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-digest" ,r-digest) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-jsonlite" ,r-jsonlite) - ("r-png" ,r-png) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson) - ("r-rsvg" ,r-rsvg) - ("r-stringi" ,r-stringi))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-base64enc + r-bh + r-biocgenerics + r-dbi + r-digest + r-dt + r-ggplot2 + r-gridextra + r-jsonlite + r-png + r-rcpp + r-rcurl + r-rjson + r-rsvg + r-stringi)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description @@ -11898,10 +11653,8 @@ structures.") (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-runit" ,r-runit))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics r-chemminer r-runit)) + (native-inputs (list r-knitr)) (home-page "https://github.com/girke-lab/fmcsR") (synopsis "Mismatch tolerant maximum common substructure searching") (description @@ -11930,15 +11683,15 @@ searching and clustering.") (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-chemminer" ,r-chemminer) - ("r-dbi" ,r-dbi) - ("r-matrix" ,r-matrix) - ("r-rjson" ,r-rjson) - ("r-rsqlite" ,r-rsqlite) - ("r-xml" ,r-xml))) + (list r-biocgenerics + r-chemminer + r-dbi + r-matrix + r-rjson + r-rsqlite + r-xml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/girke-lab/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description @@ -11965,12 +11718,9 @@ available bioactivity data.") (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-broom" ,r-broom) - ("r-dplyr" ,r-dplyr) - ("r-tidyr" ,r-tidyr))) + (list r-biobase r-broom r-dplyr r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/StoreyLab/biobroom") (synopsis "Turn Bioconductor objects into tidy data frames") (description @@ -11997,11 +11747,7 @@ visualize bioinformatics analyses.") (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-checkmate" ,r-checkmate) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-rappdirs" ,r-rappdirs))) + (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -12024,16 +11770,16 @@ symbols).") (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dose" ,r-dose) - ("r-enrichplot" ,r-enrichplot) - ("r-ggplot2" ,r-ggplot2) - ("r-ggraph" ,r-ggraph) - ("r-graphite" ,r-graphite) - ("r-igraph" ,r-igraph) - ("r-reactome-db" ,r-reactome-db))) + (list r-annotationdbi + r-dose + r-enrichplot + r-ggplot2 + r-ggraph + r-graphite + r-igraph + r-reactome-db)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/ReactomePA") (synopsis "Reactome pathway analysis") (description @@ -12056,9 +11802,7 @@ enrichment analysis and several functions for visualization.") (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-cluster" ,r-cluster) - ("r-lattice" ,r-lattice))) + (list r-biobase r-cluster r-lattice)) (home-page "https://bioconductor.org/packages/EBarrays/") (synopsis "Gene clustering and differential expression identification") (description @@ -12080,7 +11824,7 @@ microarray data.") (properties `((upstream-name . "BiocCaseStudies"))) (build-system r-build-system) - (propagated-inputs `(("r-biobase" ,r-biobase))) + (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/BiocCaseStudies") (synopsis "Support for the case studies monograph") (description @@ -12102,16 +11846,16 @@ monograph.") `((upstream-name . "BiocCheck"))) (build-system r-build-system) (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) + (list r-codetools + r-graph + r-httr + r-knitr + r-optparse + r-biocmanager + r-biocviews + r-stringdist)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocCheck") (synopsis "Executes Bioconductor-specific package checks") (description "This package contains tools to perform additional quality @@ -12132,10 +11876,7 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-geneplotter" ,r-geneplotter) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biocgenerics r-geneplotter r-graph r-rgraphviz)) (home-page "https://bioconductor.org/packages/biocGraph/") (synopsis "Graph examples and use cases in Bioinformatics") (description @@ -12157,13 +11898,9 @@ different graph related packages produced by Bioconductor.") `((upstream-name . "BiocStyle"))) (build-system r-build-system) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-bookdown" ,r-bookdown) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) + (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocStyle") (synopsis "Bioconductor formatting styles") (description "This package provides standard formatting styles for @@ -12185,13 +11922,13 @@ functionality.") `((upstream-name . "biocViews"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-graph" ,r-graph) - ("r-rbgl" ,r-rbgl) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml) - ("r-runit" ,r-runit))) + (list r-biobase + r-biocmanager + r-graph + r-rbgl + r-rcurl + r-xml + r-runit)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") (description "The purpose of biocViews is to create HTML pages that @@ -12213,15 +11950,15 @@ also known as views, in a controlled vocabulary.") (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocmanager" ,r-biocmanager) - ("r-curl" ,r-curl) - ("r-rappdirs" ,r-rappdirs) - ("r-s4vectors" ,r-s4vectors))) + (list r-annotationhub + r-biocfilecache + r-biocgenerics + r-biocmanager + r-curl + r-rappdirs + r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ExperimentHub/") (synopsis "Client to access ExperimentHub resources") (description @@ -12247,13 +11984,13 @@ access.") (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs - `(("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-mass + r-rtracklayer + r-s4vectors)) (home-page "https://github.com/Kraus-Lab/groHMM") (synopsis "GRO-seq analysis pipeline") (description @@ -12275,15 +12012,15 @@ access.") `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tidyr" ,r-tidyr))) + (list r-biobase + r-biocgenerics + r-genomicranges + r-iranges + r-s4vectors + r-summarizedexperiment + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -12309,30 +12046,30 @@ rownames.") (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs - `(("r-bigrquery" ,r-bigrquery) - ("r-car" ,r-car) - ("r-complexheatmap" ,r-complexheatmap) - ("r-curatedtcgadata" ,r-curatedtcgadata) - ("r-dbi" ,r-dbi) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-iranges" ,r-iranges) - ("r-magrittr" ,r-magrittr) - ("r-plyr" ,r-plyr) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjson" ,r-rjson) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-bigrquery + r-car + r-complexheatmap + r-curatedtcgadata + r-dbi + r-dplyr + r-dt + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-ggpubr + r-graph + r-httr + r-iranges + r-magrittr + r-plyr + r-rgraphviz + r-rjson + r-s4vectors + r-scales + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocOncoTK") (synopsis "Bioconductor components for general cancer genomics") (description @@ -12354,11 +12091,9 @@ tools for genome-scale analysis of cancer studies.") (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix))) + (list r-biocparallel r-gseabase r-matrix)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://llrs.github.io/BioCor/") (synopsis "Functional similarities") (description @@ -12383,30 +12118,30 @@ gene selection, testing relationships, and so on.") (properties `((upstream-name . "BiocPkgTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-dplyr" ,r-dplyr) - ("r-dt" ,r-dt) - ("r-gh" ,r-gh) - ("r-graph" ,r-graph) - ("r-htmltools" ,r-htmltools) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-magrittr" ,r-magrittr) - ("r-rbgl" ,r-rbgl) - ("r-readr" ,r-readr) - ("r-rlang" ,r-rlang) - ("r-rvest" ,r-rvest) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-biocmanager + r-biocviews + r-dplyr + r-dt + r-gh + r-graph + r-htmltools + r-htmlwidgets + r-httr + r-igraph + r-jsonlite + r-magrittr + r-rbgl + r-readr + r-rlang + r-rvest + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/seandavi/BiocPkgTools") (synopsis "Collection of tools for learning about Bioconductor packages") (description @@ -12431,18 +12166,18 @@ analytics on packages.") (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocio" ,r-biocio) - ("r-dplyr" ,r-dplyr) - ("r-keggrest" ,r-keggrest) - ("r-ontologyindex" ,r-ontologyindex) - ("r-plyr" ,r-plyr) - ("r-rlang" ,r-rlang) - ("r-s4vectors" ,r-s4vectors) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr))) + (list r-annotationdbi + r-biocio + r-dplyr + r-keggrest + r-ontologyindex + r-plyr + r-rlang + r-s4vectors + r-tibble + r-tidyr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocSet") (synopsis @@ -12470,17 +12205,17 @@ accessing web references for elements/sets are also available in BiocSet.") `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biocstyle" ,r-biocstyle) - ("r-bookdown" ,r-bookdown) - ("r-git2r" ,r-git2r) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rstudioapi" ,r-rstudioapi) - ("r-stringr" ,r-stringr) - ("r-usethis" ,r-usethis))) + (list r-biocstyle + r-bookdown + r-git2r + r-httr + r-knitr + r-rmarkdown + r-rstudioapi + r-stringr + r-usethis)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") (synopsis "Tools to aid the development of Bioconductor Workflow packages") (description @@ -12502,8 +12237,7 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-kernsmooth" ,r-kernsmooth))) + (list r-biobase r-kernsmooth)) (home-page "https://bioconductor.org/packages/bioDist/") (synopsis "Different distance measures") (description @@ -12525,21 +12259,21 @@ distance measures.") (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-cowplot" ,r-cowplot) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-lattice" ,r-lattice) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-reshape2" ,r-reshape2))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocparallel + r-biocsingular + r-cowplot + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-ggplot2 + r-ggrepel + r-lattice + r-matrix + r-rcpp + r-reshape2)) + (native-inputs (list r-knitr)) (home-page "https://github.com/kevinblighe/PCAtools") (synopsis "PCAtools: everything Principal Components Analysis") (description @@ -12571,12 +12305,8 @@ dimensional mass cytometry data.") (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-getoptlong" ,r-getoptlong) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-rjson" ,r-rjson))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson)) + (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/rGREAT") (synopsis "Client for GREAT analysis") (description @@ -12599,17 +12329,17 @@ user's input and automatically retrieving results from GREAT web server.") (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-corpcor" ,r-corpcor) - ("r-doparallel" ,r-doparallel) - ("r-dosnow" ,r-dosnow) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-matrix" ,r-matrix) - ("r-matrixcalc" ,r-matrixcalc) - ("r-rtsne" ,r-rtsne) - ("r-umap" ,r-umap))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-cluster + r-corpcor + r-doparallel + r-dosnow + r-foreach + r-ggplot2 + r-matrix + r-matrixcalc + r-rtsne + r-umap)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/M3C") (synopsis "Monte Carlo reference-based consensus clustering") (description @@ -12632,7 +12362,7 @@ hypothesis @code{K=1}.") (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs - `(("r-survival" ,r-survival))) + (list r-survival)) (home-page "https://bioconductor.org/packages/Icens") (synopsis "NPMLE for censored and truncated data") (description @@ -12657,10 +12387,7 @@ truncated data.") (properties `((upstream-name . "interval"))) (build-system r-build-system) (propagated-inputs - `(("r-icens" ,r-icens) - ("r-mlecens" ,r-mlecens) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-icens r-mlecens r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/interval/") (synopsis "Weighted Logrank tests and NPMLE for interval censored data") (description @@ -12684,11 +12411,7 @@ plot them, and perform logrank or Wilcoxon type tests.") (properties `((upstream-name . "FHtest"))) (build-system r-build-system) (propagated-inputs - `(("r-interval" ,r-interval) - ("r-kmsurv" ,r-kmsurv) - ("r-mass" ,r-mass) - ("r-perm" ,r-perm) - ("r-survival" ,r-survival))) + (list r-interval r-kmsurv r-mass r-perm r-survival)) (home-page "https://cran.r-project.org/web/packages/FHtest/") (synopsis "Tests for survival data based on the Fleming-Harrington class") (description @@ -12717,23 +12440,23 @@ with: (properties `((upstream-name . "FourCSeq"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-fda" ,r-fda) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbio" ,r-ggbio) - ("r-ggplot2" ,r-ggplot2) - ("r-gtools" ,r-gtools) - ("r-lsd" ,r-lsd) - ("r-matrix" ,r-matrix) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biostrings + r-deseq2 + r-fda + r-genomicalignments + r-genomicranges + r-ggbio + r-ggplot2 + r-gtools + r-lsd + r-matrix + r-reshape2 + r-rsamtools + r-rtracklayer + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html") (synopsis "Analysis of multiplexed 4C sequencing data") @@ -12783,7 +12506,7 @@ routines.") `((upstream-name . "S4Vectors"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) + (list r-biocgenerics)) (home-page "https://bioconductor.org/packages/S4Vectors") (synopsis "S4 implementation of vectors and lists") (description @@ -12812,18 +12535,18 @@ S4Vectors package itself.") (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-doparallel" ,r-doparallel) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-fastcluster" ,r-fastcluster) - ("r-foreach" ,r-foreach) - ("r-go-db" ,r-go-db) - ("r-hmisc" ,r-hmisc) - ("r-impute" ,r-impute) - ("r-rcpp" ,r-rcpp) - ("r-survival" ,r-survival) - ("r-matrixstats" ,r-matrixstats) - ("r-preprocesscore" ,r-preprocesscore))) + (list r-annotationdbi + r-doparallel + r-dynamictreecut + r-fastcluster + r-foreach + r-go-db + r-hmisc + r-impute + r-rcpp + r-survival + r-matrixstats + r-preprocesscore)) (home-page "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/") (synopsis "Weighted correlation network analysis") @@ -12862,11 +12585,11 @@ data manipulation and visualization.") ;; FIXME: Rgraphviz bundles the sources of an older variant of ;; graphviz. It does not build with the latest version of graphviz, so ;; we do not add graphviz to the inputs. - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-graph" ,r-graph))) + (list r-graph)) (native-inputs - `(("pkg-config" ,pkg-config))) + (list pkg-config)) (home-page "https://bioconductor.org/packages/Rgraphviz") (synopsis "Plotting capabilities for R graph objects") (description @@ -12887,11 +12610,9 @@ objects from the @code{graph} package.") (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs - `(("r-data-table" ,r-data-table) - ("r-fdrtool" ,r-fdrtool) - ("r-rcpp" ,r-rcpp))) + (list r-data-table r-fdrtool r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/FitHiC") (synopsis "Confidence estimation for intra-chromosomal contact maps") (description @@ -12913,13 +12634,13 @@ assays such as Hi-C.") (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-biostrings + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcolorbrewer + r-rtracklayer)) (home-page "https://bioconductor.org/packages/HiTC") (synopsis "High throughput chromosome conformation capture analysis") (description @@ -12943,16 +12664,16 @@ provided.") (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rhdf5" ,r-rhdf5) - ("r-rhdf5filters" ,r-rhdf5filters) - ("r-rhdf5lib" ,r-rhdf5lib) - ("r-s4vectors" ,r-s4vectors))) + (list zlib)) + (propagated-inputs + (list r-biocgenerics + r-delayedarray + r-iranges + r-matrix + r-rhdf5 + r-rhdf5filters + r-rhdf5lib + r-s4vectors)) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") (description "This package provides an array-like container for convenient @@ -13032,8 +12753,7 @@ block processing.") (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))))))) (propagated-inputs - `(("hdf5" ,hdf5-1.10) - ("zlib" ,zlib))) + (list hdf5-1.10 zlib)) (native-inputs `(("hdf5-source" ,(package-source hdf5-1.10)) ("r-knitr" ,r-knitr))) @@ -13056,12 +12776,9 @@ packages.") "1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp))) + (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/beachmat") (synopsis "Compiling Bioconductor to handle each matrix type") (description "This package provides a consistent C++ class interface for a @@ -13084,29 +12801,29 @@ matrices.") (base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-iranges" ,r-iranges) - ("r-keggrest" ,r-keggrest) - ("r-powerlaw" ,r-powerlaw) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-reshape2" ,r-reshape2) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (inputs (list zlib)) + (propagated-inputs + (list r-annotate + r-biocgenerics + r-biostrings + r-dbi + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-go-db + r-iranges + r-keggrest + r-powerlaw + r-r-utils + r-readr + r-reshape2 + r-rsqlite + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/ge11232002/CNEr") (synopsis "CNE Detection and Visualization") (description @@ -13134,27 +12851,27 @@ advanced visualization of sets of conserved noncoding elements.") (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-catools" ,r-catools) - ("r-cner" ,r-cner) - ("r-dbi" ,r-dbi) - ("r-dirichletmultinomial" ,r-dirichletmultinomial) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-seqlogo" ,r-seqlogo) - ("r-tfmpvalue" ,r-tfmpvalue) - ("r-xml" ,r-xml) - ("r-xvector" ,r-xvector))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-catools + r-cner + r-dbi + r-dirichletmultinomial + r-genomeinfodb + r-genomicranges + r-gtools + r-iranges + r-rsqlite + r-rtracklayer + r-s4vectors + r-seqlogo + r-tfmpvalue + r-xml + r-xvector)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ge11232002/TFBSTools") (synopsis "Transcription factor binding site (TFBS) analysis") (description @@ -13180,19 +12897,19 @@ provides a wrapper of de novo motif discovery software.") (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs - `(("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biostrings + r-bsgenome + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-rcpp + r-rcpparmadillo + r-rsamtools + r-s4vectors + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/motifmatchr") (synopsis "Fast motif matching in R") (description @@ -13213,29 +12930,29 @@ This package wraps C++ code from the MOODS motif calling library.") (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dt" ,r-dt) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-miniui" ,r-miniui) - ("r-nabor" ,r-nabor) - ("r-plotly" ,r-plotly) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rsamtools" ,r-rsamtools) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tfbstools" ,r-tfbstools))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-matrix + r-miniui + r-nabor + r-plotly + r-rcolorbrewer + r-rcpp + r-rcpparmadillo + r-rsamtools + r-rtsne + r-s4vectors + r-shiny + r-summarizedexperiment + r-tfbstools)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") (synopsis "Determine chromatin variation across regions") (description @@ -13262,13 +12979,10 @@ sequence (@code{DNAse-seq}) experiments.") `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray) - ("r-genomicranges" ,r-genomicranges) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors + r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/SingleCellExperiment") (synopsis "S4 classes for single cell data") (description "This package defines an S4 class for storing data from @@ -13292,18 +13006,18 @@ libraries.") (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomicranges" ,r-genomicranges) - ("r-matrix" ,r-matrix) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocparallel + r-delayedarray + r-delayedmatrixstats + r-genomicranges + r-matrix + r-rcpp + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/scuttle") (synopsis "Single-cell RNA-Seq analysis utilities") (description @@ -13325,28 +13039,28 @@ of other packages.") "0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocneighbors" ,r-biocneighbors) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-gridextra" ,r-gridextra) - ("r-matrix" ,r-matrix) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rlang" ,r-rlang) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biocgenerics + r-biocneighbors + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-ggbeeswarm + r-ggplot2 + r-ggrepel + r-gridextra + r-matrix + r-rcolorbrewer + r-rlang + r-rtsne + r-s4vectors + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/davismcc/scater") (synopsis "Single-cell analysis toolkit for gene expression data in R") (description "This package provides a collection of tools for doing @@ -13367,28 +13081,28 @@ quality control.") "06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic")))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-bh" ,r-bh) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biocsingular" ,r-biocsingular) - ("r-bluster" ,r-bluster) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dqrng" ,r-dqrng) - ("r-edger" ,r-edger) - ("r-igraph" ,r-igraph) - ("r-limma" ,r-limma) - ("r-matrix" ,r-matrix) - ("r-metapod" ,r-metapod) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors) - ("r-scuttle" ,r-scuttle) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-statmod" ,r-statmod) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-bh + r-biocgenerics + r-biocparallel + r-biocsingular + r-bluster + r-delayedarray + r-delayedmatrixstats + r-dqrng + r-edger + r-igraph + r-limma + r-matrix + r-metapod + r-rcpp + r-s4vectors + r-scuttle + r-singlecellexperiment + r-statmod + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -13412,11 +13126,8 @@ variable and significantly correlated genes.") `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-rcpp" ,r-rcpp))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-matrix r-matrixgenerics r-matrixstats r-rcpp)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/sparseMatrixStats/") (synopsis "Summary statistics for rows and columns of sparse matrices") (description @@ -13440,15 +13151,15 @@ data in the column sparse format.") `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) (propagated-inputs - `(("r-delayedarray" ,r-delayedarray) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-matrixstats" ,r-matrixstats) - ("r-s4vectors" ,r-s4vectors) - ("r-sparsematrixstats" ,r-sparsematrixstats))) + (list r-delayedarray + r-iranges + r-matrix + r-matrixgenerics + r-matrixstats + r-s4vectors + r-sparsematrixstats)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") (description @@ -13475,12 +13186,9 @@ memory usage and processing time is minimized.") (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs - `(("r-clue" ,r-clue) - ("r-mass" ,r-mass) - ("r-rcpp" ,r-rcpp) - ("r-s4vectors" ,r-s4vectors))) + (list r-clue r-mass r-rcpp r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils") (synopsis "Core utils for mass spectrometry data") (description @@ -13506,11 +13214,9 @@ within the R for Mass Spectrometry packages.") (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs - `(("r-mscoreutils" ,r-mscoreutils) - ("r-protgenerics" ,r-protgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment))) + (list r-mscoreutils r-protgenerics r-summarizedexperiment)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/RforMassSpectrometry/MsFeatures") (synopsis "Functionality for mass spectrometry features") (description @@ -13539,10 +13245,9 @@ the respective packages (such as e.g. @code{xcms}).") (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) + (list r-biocgenerics r-s4vectors)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocIO") (synopsis "Standard input and output for Bioconductor packages") (description @@ -13573,10 +13278,7 @@ as well as local access. Developers can register a file extension, e.g., (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs - `(("r-gplots" ,r-gplots) - ("r-mass" ,r-mass) - ("r-msnbase" ,r-msnbase) - ("r-rcolorbrewer" ,r-rcolorbrewer))) + (list r-gplots r-mass r-msnbase r-rcolorbrewer)) (home-page "https://bioconductor.org/packages/msmsEDA") (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts") @@ -13599,10 +13301,7 @@ experiments, and visualize de influence of the involved factors.") (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs - `(("r-edger" ,r-edger) - ("r-msmseda" ,r-msmseda) - ("r-msnbase" ,r-msnbase) - ("r-qvalue" ,r-qvalue))) + (list r-edger r-msmseda r-msnbase r-qvalue)) (home-page "https://bioconductor.org/packages/msmsTests") (synopsis "Differential LC-MS/MS expression tests") @@ -13631,34 +13330,34 @@ relevant, and the minimum expression of the most abundant condition.") (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs - `(("r-circlize" ,r-circlize) - ("r-complexheatmap" ,r-complexheatmap) - ("r-consensusclusterplus" ,r-consensusclusterplus) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-drc" ,r-drc) - ("r-flowcore" ,r-flowcore) - ("r-flowsom" ,r-flowsom) - ("r-ggplot2" ,r-ggplot2) - ("r-ggrepel" ,r-ggrepel) - ("r-ggridges" ,r-ggridges) - ("r-gridextra" ,r-gridextra) - ("r-magrittr" ,r-magrittr) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-nnls" ,r-nnls) - ("r-purrr" ,r-purrr) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-rtsne" ,r-rtsne) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-scater" ,r-scater) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-circlize + r-complexheatmap + r-consensusclusterplus + r-cowplot + r-data-table + r-dplyr + r-drc + r-flowcore + r-flowsom + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-magrittr + r-matrix + r-matrixstats + r-nnls + r-purrr + r-rcolorbrewer + r-reshape2 + r-rtsne + r-s4vectors + r-scales + r-scater + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") @@ -13688,22 +13387,22 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.") "0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biocparallel + r-genomeinfodb + r-genomicfiles + r-genomicranges + r-ggplot2 + r-homo-sapiens + r-iranges + r-rtracklayer + r-s4vectors + r-shiny + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/erma") (synopsis "Epigenomic road map adventures") (description @@ -13738,35 +13437,35 @@ by Ernst and Kellis.") (("fechable") "fetchable")) #t))))) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationfilter" ,r-annotationfilter) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggally" ,r-ggally) - ("r-ggplot2" ,r-ggplot2) - ("r-gridextra" ,r-gridextra) - ("r-gtable" ,r-gtable) - ("r-hmisc" ,r-hmisc) - ("r-iranges" ,r-iranges) - ("r-organismdbi" ,r-organismdbi) - ("r-reshape2" ,r-reshape2) - ("r-rlang" ,r-rlang) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationfilter + r-biobase + r-biocgenerics + r-biostrings + r-biovizbase + r-bsgenome + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-ggally + r-ggplot2 + r-gridextra + r-gtable + r-hmisc + r-iranges + r-organismdbi + r-reshape2 + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-scales + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "http://www.tengfei.name/ggbio/") (synopsis "Visualization tools for genomic data") (description @@ -13804,21 +13503,21 @@ interval to data view, mismatch pileup, and several splicing summaries.") (("importFrom\\(ff,.*") "import(ff)\n")) #t))))) (propagated-inputs - `(("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-biocgenerics" ,r-biocgenerics) - ("r-bit" ,r-bit) - ("r-doparallel" ,r-doparallel) - ("r-ff" ,r-ff) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-batchjobs + r-bbmisc + r-biocgenerics + r-bit + r-doparallel + r-ff + r-ffbase + r-foreach + r-genomicfiles + r-genomicranges + r-rtracklayer + r-s4vectors + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description @@ -13841,38 +13540,38 @@ and more.") (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-batchjobs" ,r-batchjobs) - ("r-bbmisc" ,r-bbmisc) - ("r-beeswarm" ,r-beeswarm) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-doparallel" ,r-doparallel) - ("r-dplyr" ,r-dplyr) - ("r-erma" ,r-erma) - ("r-ffbase" ,r-ffbase) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggbeeswarm" ,r-ggbeeswarm) - ("r-ggplot2" ,r-ggplot2) - ("r-gqtlbase" ,r-gqtlbase) - ("r-hardyweinberg" ,r-hardyweinberg) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-mgcv" ,r-mgcv) - ("r-plotly" ,r-plotly) - ("r-reshape2" ,r-reshape2) - ("r-s4vectors" ,r-s4vectors) - ("r-shiny" ,r-shiny) - ("r-snpstats" ,r-snpstats) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-batchjobs + r-bbmisc + r-beeswarm + r-biobase + r-biocgenerics + r-doparallel + r-dplyr + r-erma + r-ffbase + r-foreach + r-genomeinfodb + r-genomicfeatures + r-genomicfiles + r-genomicranges + r-ggbeeswarm + r-ggplot2 + r-gqtlbase + r-hardyweinberg + r-homo-sapiens + r-iranges + r-limma + r-mgcv + r-plotly + r-reshape2 + r-s4vectors + r-shiny + r-snpstats + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gQTLstats") (synopsis "Computationally efficient analysis for eQTL and allied studies") (description @@ -13897,30 +13596,30 @@ family of feature/genome hypotheses.") (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-biovizbase" ,r-biovizbase) - ("r-bsgenome" ,r-bsgenome) - ("r-digest" ,r-digest) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-matrixstats" ,r-matrixstats) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-biobase + r-biocgenerics + r-biomart + r-biostrings + r-biovizbase + r-bsgenome + r-digest + r-ensembldb + r-genomeinfodb + r-genomicalignments + r-genomicfeatures + r-genomicranges + r-iranges + r-lattice + r-latticeextra + r-matrixstats + r-rcolorbrewer + r-rsamtools + r-rtracklayer + r-s4vectors + r-xvector)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description @@ -13945,20 +13644,20 @@ with your data.") "0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx")))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-readr" ,r-readr) - ("r-s4vectors" ,r-s4vectors) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-readr + r-s4vectors + r-snpstats + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description @@ -13979,10 +13678,7 @@ EMBL-EBI GWAS catalog.") (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs - `(("r-graph" ,r-graph) - ("r-rcurl" ,r-rcurl) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-graph r-rcurl r-rgraphviz r-xml)) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description @@ -14006,18 +13702,18 @@ functionalities including parsing, graph operation, visualization and etc.") "1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg")))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfiles" ,r-genomicfiles) - ("r-httr" ,r-httr) - ("r-matrix" ,r-matrix) - ("r-rsamtools" ,r-rsamtools) - ("r-snpstats" ,r-snpstats) - ("r-variantannotation" ,r-variantannotation))) + (list r-biocgenerics + r-ensdb-hsapiens-v75 + r-ensembldb + r-genomeinfodb + r-genomicfiles + r-httr + r-matrix + r-rsamtools + r-snpstats + r-variantannotation)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description @@ -14043,9 +13739,7 @@ defining LD blocks.") (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs - `(("r-genetics" ,r-genetics) - ("r-rcpp" ,r-rcpp) - ("r-snpstats" ,r-snpstats))) + (list r-genetics r-rcpp r-snpstats)) (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description @@ -14070,14 +13764,14 @@ on the plot.") "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) (build-system r-build-system) (inputs - `(("gsl" ,gsl))) - (propagated-inputs - `(("r-lme4" ,r-lme4) - ("r-nnet" ,r-nnet) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rjags" ,r-rjags))) + (list gsl)) + (propagated-inputs + (list r-lme4 + r-nnet + r-rcpp + r-rcpparmadillo + r-rgraphviz + r-rjags)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -14107,12 +13801,9 @@ statistical dependencies in messy, complex data.") "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w")))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + (list zlib)) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-catools" ,r-catools) - ("r-rcpp" ,r-rcpp) - ("r-rsamtools" ,r-rsamtools))) + (list r-bh r-catools r-rcpp r-rsamtools)) (home-page "https://cran.r-project.org/web/packages/spp/") (synopsis "ChIP-Seq processing pipeline") (description "This package provides tools for analysis of ChIP-seq and @@ -14132,14 +13823,14 @@ other functional sequencing data.") (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-graph" ,r-graph) - ("r-kegggraph" ,r-kegggraph) - ("r-keggrest" ,r-keggrest) - ("r-org-hs-eg-db" ,r-org-hs-eg-db) - ("r-png" ,r-png) - ("r-rgraphviz" ,r-rgraphviz) - ("r-xml" ,r-xml))) + (list r-annotationdbi + r-graph + r-kegggraph + r-keggrest + r-org-hs-eg-db + r-png + r-rgraphviz + r-xml)) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description @@ -14166,12 +13857,9 @@ large-scale and fully automated analysis.") "0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) - (inputs `(("zlib" ,zlib))) + (inputs (list zlib)) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-matrix" ,r-matrix) - ("r-survival" ,r-survival) - ("r-zlibbioc" ,r-zlibbioc))) + (list r-biocgenerics r-matrix r-survival r-zlibbioc)) (home-page "https://bioconductor.org/packages/snpStats") (synopsis "Methods for SNP association studies") (description @@ -14194,21 +13882,21 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs - `(("r-bamsignals" ,r-bamsignals) - ("r-biocgenerics" ,r-biocgenerics) - ("r-chromstardata" ,r-chromstardata) - ("r-doparallel" ,r-doparallel) - ("r-foreach" ,r-foreach) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm) - ("r-reshape2" ,r-reshape2) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-bamsignals + r-biocgenerics + r-chromstardata + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-iranges + r-mvtnorm + r-reshape2 + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://github.com/ataudt/chromstaR") (synopsis "Chromatin state analysis for ChIP-Seq data") (description @@ -14232,16 +13920,16 @@ analyses.") (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-knitr" ,r-knitr) - ("r-magrittr" ,r-magrittr) - ("r-rtracklayer" ,r-rtracklayer))) + (list r-annotationdbi + r-dplyr + r-genomicfeatures + r-genomicranges + r-ggplot2 + r-knitr + r-magrittr + r-rtracklayer)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/Guitar") (synopsis "Visualize genomic features") (description @@ -14263,8 +13951,7 @@ starting site, start codon, stop codon and transcription ending site.") (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs - `(("r-biomart" ,r-biomart) - ("r-zoo" ,r-zoo))) + (list r-biomart r-zoo)) (home-page "https://bioconductor.org/packages/Sushi") (synopsis "Tools for visualizing genomics data") (description @@ -14286,17 +13973,17 @@ visualizations for publication-quality multi-panel figures.") (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-sva" ,r-sva))) + (list r-biobase + r-genomeinfodb + r-genomicranges + r-iranges + r-limma + r-rcolorbrewer + r-rtracklayer + r-s4vectors + r-sva)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://bioconductor.org/packages/ballgown") (synopsis "Flexible, isoform-level differential expression analysis") (description @@ -14319,17 +14006,17 @@ to annotation.") "0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) - (inputs `(("megadepth" ,megadepth))) + (inputs (list megadepth)) (propagated-inputs - `(("r-cmdfun" ,r-cmdfun) - ("r-dplyr" ,r-dplyr) - ("r-fs" ,r-fs) - ("r-genomicranges" ,r-genomicranges) - ("r-magrittr" ,r-magrittr) - ("r-readr" ,r-readr) - ("r-xfun" ,r-xfun))) + (list r-cmdfun + r-dplyr + r-fs + r-genomicranges + r-magrittr + r-readr + r-xfun)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/LieberInstitute/megadepth") (synopsis "BigWig and BAM related utilities") (description @@ -14353,16 +14040,16 @@ regions or annotations of your choice from BigWig files.") (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs - `(("r-abind" ,r-abind) - ("r-biocparallel" ,r-biocparallel) - ("r-data-table" ,r-data-table) - ("r-futile-logger" ,r-futile-logger) - ("r-matrix" ,r-matrix) - ("r-outliers" ,r-outliers) - ("r-rcpp" ,r-rcpp) - ("r-rdpack" ,r-rdpack))) + (list r-abind + r-biocparallel + r-data-table + r-futile-logger + r-matrix + r-outliers + r-rcpp + r-rdpack)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/uds-helms/BEclear") (synopsis "Correction of batch effects in DNA methylation data") (description @@ -14386,19 +14073,19 @@ real numbers.") (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs - `(("kallisto" ,kallisto) - ("r-biomart" ,r-biomart) - ("r-biostrings" ,r-biostrings) - ("r-data-table" ,r-data-table) - ("r-dplyr" ,r-dplyr) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-jsonlite" ,r-jsonlite) - ("r-rhdf5" ,r-rhdf5) - ("r-rslurm" ,r-rslurm) - ("r-rtracklayer" ,r-rtracklayer) - ("r-sjmisc" ,r-sjmisc) - ("r-tximport" ,r-tximport))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list kallisto + r-biomart + r-biostrings + r-data-table + r-dplyr + r-genomicfeatures + r-jsonlite + r-rhdf5 + r-rslurm + r-rtracklayer + r-sjmisc + r-tximport)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeCall") (synopsis "RNA-Seq present/absent gene expression calls generation") (description @@ -14422,18 +14109,18 @@ all RNA-Seq libraries of each species integrated in Bgee.") (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-curl" ,r-curl) - ("r-data-table" ,r-data-table) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-graph" ,r-graph) - ("r-r-utils" ,r-r-utils) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-tidyr" ,r-tidyr) - ("r-topgo" ,r-topgo))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biobase + r-curl + r-data-table + r-digest + r-dplyr + r-graph + r-r-utils + r-rcurl + r-rsqlite + r-tidyr + r-topgo)) + (native-inputs (list r-knitr)) (home-page "https://github.com/BgeeDB/BgeeDB_R") (synopsis "Annotation and gene expression data retrieval from Bgee database") (description @@ -14456,11 +14143,8 @@ anatomical terms, mapped to genes by expression patterns.") (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs - `(("r-httpuv" ,r-httpuv) - ("r-httr" ,r-httr) - ("r-jsonlite" ,r-jsonlite) - ("r-stringi" ,r-stringi))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-httpuv r-httr r-jsonlite r-stringi)) + (native-inputs (list r-knitr)) (home-page "https://github.com/tamerh/biobtreeR") (synopsis "Use biobtree tool from R") (description @@ -14483,7 +14167,7 @@ mappings functionalities.") (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs - `(("r-infotheo" ,r-infotheo))) + (list r-infotheo)) (home-page "http://minet.meyerp.com") (synopsis "Mutual information networks") (description @@ -14506,10 +14190,7 @@ information networks from data.") `((upstream-name . "geNetClassifier"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-e1071" ,r-e1071) - ("r-ebarrays" ,r-ebarrays) - ("r-minet" ,r-minet))) + (list r-biobase r-e1071 r-ebarrays r-minet)) (home-page "https://www.cicancer.org") (synopsis "Classify diseases and build gene networks using expression profiles") (description @@ -14532,8 +14213,8 @@ interface to query the classifier.") "1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) - (propagated-inputs `(("r-filelock" ,r-filelock))) - (native-inputs `(("r-knitr" ,r-knitr))) + (propagated-inputs (list r-filelock)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/dir.expiry") (synopsis "Managing expiration for cache directories") (description @@ -14558,8 +14239,8 @@ eliminating obsolete caches generated by old versions of packages.") `((upstream-name . "basilisk.utils"))) (build-system r-build-system) (propagated-inputs - `(("r-dir-expiry" ,r-dir-expiry))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-dir-expiry)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk.utils") (synopsis "Basilisk installation utilities") (description @@ -14581,10 +14262,8 @@ package, primarily for creation of the underlying Conda instance.") (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs - `(("r-basilisk-utils" ,r-basilisk-utils) - ("r-dir-expiry" ,r-dir-expiry) - ("r-reticulate" ,r-reticulate))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-basilisk-utils r-dir-expiry r-reticulate)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/basilisk") (synopsis "Freeze Python dependencies inside Bioconductor packages") (description @@ -14614,13 +14293,13 @@ Python environments in a single R session.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-fs" ,r-fs) - ("r-glue" ,r-glue) - ("r-rlang" ,r-rlang) - ("r-styler" ,r-styler) - ("r-usethis" ,r-usethis))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocmanager + r-fs + r-glue + r-rlang + r-styler + r-usethis)) + (native-inputs (list r-knitr)) (home-page "https://github.com/lcolladotor/biocthis") (synopsis "Automate package and project setup for Bioconductor packages") (description @@ -14644,13 +14323,13 @@ Bioconductor-friendly.") `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) (propagated-inputs - `(("docker" ,docker) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-memoise" ,r-memoise) - ("r-readr" ,r-readr) - ("r-whisker" ,r-whisker))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list docker + r-dplyr + r-httr + r-memoise + r-readr + r-whisker)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocDockerManager") (synopsis "Access and manage Bioconductor Docker images") (description @@ -14673,25 +14352,25 @@ the Bioconductor project.") (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs - `(("r-biocfilecache" ,r-biocfilecache) - ("r-chk" ,r-chk) - ("r-jsonlite" ,r-jsonlite) - ("r-lgr" ,r-lgr) - ("r-lifecycle" ,r-lifecycle) - ("r-openssl" ,r-openssl) - ("r-plyr" ,r-plyr) - ("r-progress" ,r-progress) - ("r-r6" ,r-r6) - ("r-rappdirs" ,r-rappdirs) - ("r-rcpp" ,r-rcpp) - ("r-rcurl" ,r-rcurl) - ("r-rsqlite" ,r-rsqlite) - ("r-stringr" ,r-stringr) - ("r-testthat" ,r-testthat) - ("r-withr" ,r-withr) - ("r-xml" ,r-xml) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-biocfilecache + r-chk + r-jsonlite + r-lgr + r-lifecycle + r-openssl + r-plyr + r-progress + r-r6 + r-rappdirs + r-rcpp + r-rcurl + r-rsqlite + r-stringr + r-testthat + r-withr + r-xml + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biodb") (synopsis "Library for connecting to chemical and biological databases") (description @@ -14718,11 +14397,8 @@ separate published packages.") (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs - `(("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-plyr" ,r-plyr) - ("r-rhdf5" ,r-rhdf5))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-jsonlite r-matrix r-plyr r-rhdf5)) + (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/biomformat/") (synopsis "Interface package for the BIOM file format") (description @@ -14770,10 +14446,7 @@ design.") (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-mvcclass" ,r-mvcclass) - ("r-rgraphviz" ,r-rgraphviz))) + (list r-biobase r-graph r-mvcclass r-rgraphviz)) (home-page "https://bioconductor.org/packages/BioMVCClass") (synopsis "Model-View-Controller (MVC) classes that use Biobase") (description @@ -14795,10 +14468,7 @@ design.") (properties `((upstream-name . "biomvRCNS"))) (build-system r-build-system) (propagated-inputs - `(("r-genomicranges" ,r-genomicranges) - ("r-gviz" ,r-gviz) - ("r-iranges" ,r-iranges) - ("r-mvtnorm" ,r-mvtnorm))) + (list r-genomicranges r-gviz r-iranges r-mvtnorm)) (home-page "https://bioconductor.org/packages/biomvRCNS") (synopsis "Copy number study and segmentation for multivariate biological data") (description @@ -14823,28 +14493,28 @@ using aCGH or sequencing.") (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-complexheatmap" ,r-complexheatmap) - ("r-deseq2" ,r-deseq2) - ("r-dynamictreecut" ,r-dynamictreecut) - ("r-genie3" ,r-genie3) - ("r-ggnetwork" ,r-ggnetwork) - ("r-ggnewscale" ,r-ggnewscale) - ("r-ggplot2" ,r-ggplot2) - ("r-ggpubr" ,r-ggpubr) - ("r-igraph" ,r-igraph) - ("r-intergraph" ,r-intergraph) - ("r-matrixstats" ,r-matrixstats) - ("r-minet" ,r-minet) - ("r-netrep" ,r-netrep) - ("r-networkd3" ,r-networkd3) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-reshape2" ,r-reshape2) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-sva" ,r-sva) - ("r-wgcna" ,r-wgcna))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-complexheatmap + r-deseq2 + r-dynamictreecut + r-genie3 + r-ggnetwork + r-ggnewscale + r-ggplot2 + r-ggpubr + r-igraph + r-intergraph + r-matrixstats + r-minet + r-netrep + r-networkd3 + r-rcolorbrewer + r-reshape2 + r-summarizedexperiment + r-sva + r-wgcna)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/almeidasilvaf/BioNERO") (synopsis "Biological network reconstruction omnibus") (description @@ -14879,11 +14549,7 @@ networks.") (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-graph" ,r-graph) - ("r-igraph" ,r-igraph) - ("r-rbgl" ,r-rbgl))) + (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl)) (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html") (synopsis "Functional analysis of biological networks") (description @@ -14912,26 +14578,26 @@ scoring subnetwork.") (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs - `(("r-biocparallel" ,r-biocparallel) - ("r-dt" ,r-dt) - ("r-ggplot2" ,r-ggplot2) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-knitr" ,r-knitr) - ("r-markdown" ,r-markdown) - ("r-pathview" ,r-pathview) - ("r-pheatmap" ,r-pheatmap) - ("r-plyr" ,r-plyr) - ("r-psych" ,r-psych) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rjsonio" ,r-rjsonio) - ("r-rmarkdown" ,r-rmarkdown) - ("r-shiny" ,r-shiny) - ("r-shinybs" ,r-shinybs) - ("r-whisker" ,r-whisker) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biocparallel + r-dt + r-ggplot2 + r-hmisc + r-igraph + r-knitr + r-markdown + r-pathview + r-pheatmap + r-plyr + r-psych + r-rcolorbrewer + r-rjsonio + r-rmarkdown + r-shiny + r-shinybs + r-whisker + r-yaml)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/jardimViniciusC/BioNetStat") (synopsis "Biological network analysis") (description @@ -14954,11 +14620,9 @@ network and metabolic pathways view.") (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-edger" ,r-edger) - ("r-rcpp" ,r-rcpp))) + (list r-biobase r-edger r-rcpp)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://accio.github.io/BioQC/") (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") (description @@ -14982,15 +14646,15 @@ optimised for high performance.") (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs - `(("r-cluster" ,r-cluster) - ("r-genomicranges" ,r-genomicranges) - ("r-hmisc" ,r-hmisc) - ("r-igraph" ,r-igraph) - ("r-mass" ,r-mass) - ("r-psych" ,r-psych) - ("r-stringr" ,r-stringr))) + (list r-cluster + r-genomicranges + r-hmisc + r-igraph + r-mass + r-psych + r-stringr)) (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-knitr)) (home-page "https://github.com/xyang2uchicago/BioTIP") (synopsis "R package for characterization of biological tipping-point") (description @@ -15012,20 +14676,20 @@ help unravel disease regulatory trajectory.") (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs - `(("r-assertthat" ,r-assertthat) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-dplyr" ,r-dplyr) - ("r-drtmle" ,r-drtmle) - ("r-ggplot2" ,r-ggplot2) - ("r-ggsci" ,r-ggsci) - ("r-limma" ,r-limma) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-superheat" ,r-superheat) - ("r-tibble" ,r-tibble))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-assertthat + r-biocgenerics + r-biocparallel + r-dplyr + r-drtmle + r-ggplot2 + r-ggsci + r-limma + r-s4vectors + r-summarizedexperiment + r-superheat + r-tibble)) + (native-inputs + (list r-knitr)) (home-page "https://code.nimahejazi.org/biotmle/") (synopsis "Targeted learning with moderated statistics for biomarker discovery") (description @@ -15054,31 +14718,31 @@ ensemble machine learning for the estimation of nuisance functions.") (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs - `(("r-beachmat" ,r-beachmat) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-permute" ,r-permute) - ("r-r-utils" ,r-r-utils) - ("r-rcpp" ,r-rcpp) - ("r-rhdf5" ,r-rhdf5) - ("r-s4vectors" ,r-s4vectors) - ("r-scales" ,r-scales) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-beachmat + r-biobase + r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome + r-data-table + r-delayedarray + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-iranges + r-limma + r-locfit + r-permute + r-r-utils + r-rcpp + r-rhdf5 + r-s4vectors + r-scales + r-summarizedexperiment)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/hansenlab/bsseq") (synopsis "Analyze, manage and store bisulfite sequencing data") (description @@ -15100,25 +14764,25 @@ visualizing bisulfite sequencing data.") (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationhub" ,r-annotationhub) - ("r-annotatr" ,r-annotatr) - ("r-biocparallel" ,r-biocparallel) - ("r-bsseq" ,r-bsseq) - ("r-bumphunter" ,r-bumphunter) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-matrixstats" ,r-matrixstats) - ("r-nlme" ,r-nlme) - ("r-outliers" ,r-outliers) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationhub + r-annotatr + r-biocparallel + r-bsseq + r-bumphunter + r-delayedmatrixstats + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-iranges + r-locfit + r-matrixstats + r-nlme + r-outliers + r-rcolorbrewer + r-rtracklayer + r-s4vectors)) + (native-inputs + (list r-knitr)) (home-page "https://bioconductor.org/packages/dmrseq") (synopsis "Detection and inference of differentially methylated regions") (description @@ -15150,30 +14814,30 @@ interest on transformed methylation proportions.") (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs - `(("r-checkmate" ,r-checkmate) - ("r-crayon" ,r-crayon) - ("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-dplyr" ,r-dplyr) - ("r-httr" ,r-httr) - ("r-igraph" ,r-igraph) - ("r-jsonlite" ,r-jsonlite) - ("r-later" ,r-later) - ("r-logger" ,r-logger) - ("r-magrittr" ,r-magrittr) - ("r-progress" ,r-progress) - ("r-purrr" ,r-purrr) - ("r-rappdirs" ,r-rappdirs) - ("r-readr" ,r-readr) - ("r-readxl" ,r-readxl) - ("r-rlang" ,r-rlang) - ("r-stringr" ,r-stringr) - ("r-tibble" ,r-tibble) - ("r-tidyr" ,r-tidyr) - ("r-tidyselect" ,r-tidyselect) - ("r-xml2" ,r-xml2) - ("r-yaml" ,r-yaml))) - (native-inputs `(("r-knitr" ,r-knitr))) + (list r-checkmate + r-crayon + r-curl + r-digest + r-dplyr + r-httr + r-igraph + r-jsonlite + r-later + r-logger + r-magrittr + r-progress + r-purrr + r-rappdirs + r-readr + r-readxl + r-rlang + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-xml2 + r-yaml)) + (native-inputs (list r-knitr)) (home-page "https://saezlab.github.io/OmnipathR/") (synopsis "OmniPath web service client and more") (description @@ -15198,34 +14862,34 @@ for ligand activity prediction from transcriptomics data.") (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biscuiteerdata" ,r-biscuiteerdata) - ("r-bsseq" ,r-bsseq) - ("r-data-table" ,r-data-table) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dmrseq" ,r-dmrseq) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-gtools" ,r-gtools) - ("r-hdf5array" ,r-hdf5array) - ("r-homo-sapiens" ,r-homo-sapiens) - ("r-impute" ,r-impute) - ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) - ("r-mus-musculus" ,r-mus-musculus) - ("r-qdnaseq" ,r-qdnaseq) - ("r-qualv" ,r-qualv) - ("r-r-utils" ,r-r-utils) - ("r-readr" ,r-readr) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-biobase + r-biocgenerics + r-biocparallel + r-biscuiteerdata + r-bsseq + r-data-table + r-delayedmatrixstats + r-dmrseq + r-genomeinfodb + r-genomicranges + r-gtools + r-hdf5array + r-homo-sapiens + r-impute + r-matrix + r-matrixstats + r-mus-musculus + r-qdnaseq + r-qualv + r-r-utils + r-readr + r-rsamtools + r-rtracklayer + r-s4vectors + r-summarizedexperiment + r-variantannotation)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/trichelab/biscuiteer") (synopsis "Convenience functions for the Biscuit package") (description @@ -15249,23 +14913,23 @@ estimates, etc.") (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-annotationhub" ,r-annotationhub) - ("r-biocfilecache" ,r-biocfilecache) - ("r-biostrings" ,r-biostrings) - ("r-ensembldb" ,r-ensembldb) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-jsonlite" ,r-jsonlite) - ("r-matrix" ,r-matrix) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-tibble" ,r-tibble) - ("r-tximport" ,r-tximport))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-annotationdbi + r-annotationhub + r-biocfilecache + r-biostrings + r-ensembldb + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-jsonlite + r-matrix + r-s4vectors + r-summarizedexperiment + r-tibble + r-tximport)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description @@ -15289,24 +14953,24 @@ reproducibility.") (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs - `(("r-ade4" ,r-ade4) - ("r-ape" ,r-ape) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biomformat" ,r-biomformat) - ("r-biostrings" ,r-biostrings) - ("r-cluster" ,r-cluster) - ("r-data-table" ,r-data-table) - ("r-foreach" ,r-foreach) - ("r-ggplot2" ,r-ggplot2) - ("r-igraph" ,r-igraph) - ("r-multtest" ,r-multtest) - ("r-plyr" ,r-plyr) - ("r-reshape2" ,r-reshape2) - ("r-scales" ,r-scales) - ("r-vegan" ,r-vegan))) - (native-inputs - `(("r-knitr" ,r-knitr))) + (list r-ade4 + r-ape + r-biobase + r-biocgenerics + r-biomformat + r-biostrings + r-cluster + r-data-table + r-foreach + r-ggplot2 + r-igraph + r-multtest + r-plyr + r-reshape2 + r-scales + r-vegan)) + (native-inputs + (list r-knitr)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description |